cert-manager: Error initializing issuer: context deadline exceeded

Describe the bug:

Failed to create clusterissuer, the following is the error log of cert-manager:

$ kubectl -n cert-manager logs -f cert-manager-59d959c87c-qsxbc
I0914 17:33:32.129086       1 controller.go:186] cert-manager/controller "msg"="starting controller" "controller"="clusterissuers" 
I0914 17:33:32.129113       1 controller.go:163] cert-manager/controller "msg"="not starting controller as it's disabled" "controller"="certificatesigningrequests-issuer-venafi" 
I0914 17:33:32.129130       1 controller.go:186] cert-manager/controller "msg"="starting controller" "controller"="certificates-revision-manager" 
I0914 17:33:32.129143       1 controller.go:163] cert-manager/controller "msg"="not starting controller as it's disabled" "controller"="certificatesigningrequests-issuer-selfsigned" 
I0914 17:33:32.129656       1 controller.go:186] cert-manager/controller "msg"="starting controller" "controller"="certificates-key-manager" 
I0914 17:33:32.129744       1 controller.go:186] cert-manager/controller "msg"="starting controller" "controller"="orders" 
I0914 17:33:32.133919       1 controller.go:186] cert-manager/controller "msg"="starting controller" "controller"="ingress-shim" 
I0914 17:33:32.133980       1 controller.go:186] cert-manager/controller "msg"="starting controller" "controller"="certificaterequests-approver" 
I0914 17:33:32.133996       1 controller.go:186] cert-manager/controller "msg"="starting controller" "controller"="certificaterequests-issuer-ca" 
I0914 17:33:32.134022       1 controller.go:186] cert-manager/controller "msg"="starting controller" "controller"="certificates-issuing" 
I0914 17:33:32.134044       1 controller.go:186] cert-manager/controller "msg"="starting controller" "controller"="certificaterequests-issuer-vault" 
I0914 17:33:32.134078       1 controller.go:186] cert-manager/controller "msg"="starting controller" "controller"="certificates-readiness" 
I0914 17:33:32.236494       1 controller.go:186] cert-manager/controller "msg"="starting controller" "controller"="challenges" 
I0914 17:33:32.236658       1 controller.go:186] cert-manager/controller "msg"="starting controller" "controller"="certificates-trigger" 
I0914 17:33:32.236691       1 controller.go:186] cert-manager/controller "msg"="starting controller" "controller"="certificates-request-manager" 
I0914 17:35:53.546363       1 setup.go:219] cert-manager/controller/clusterissuers "msg"="ACME server URL host and ACME private key registration host differ. Re-checking ACME account registration" "related_resource_kind"="Secret" "related_resource_name"="letsencrypt-staging" "related_resource_namespace"="cert-manager" "resource_kind"="ClusterIssuer" "resource_name"="letsencrypt-staging" "resource_namespace"="" "resource_version"="v1" 
E0914 17:36:03.547090       1 setup.go:259] cert-manager/controller/clusterissuers "msg"="failed to register an ACME account" "error"="context deadline exceeded" "related_resource_kind"="Secret" "related_resource_name"="letsencrypt-staging" "related_resource_namespace"="cert-manager" "resource_kind"="ClusterIssuer" "resource_name"="letsencrypt-staging" "resource_namespace"="" "resource_version"="v1" 
I0914 17:36:03.547134       1 conditions.go:95] Setting lastTransitionTime for Issuer "letsencrypt-staging" condition "Ready" to 2021-09-14 17:36:03.547122659 +0800 CST m=+151.486801748
E0914 17:36:03.547165       1 sync.go:60] cert-manager/controller/clusterissuers "msg"="error setting up issuer" "error"="context deadline exceeded" "resource_kind"="ClusterIssuer" "resource_name"="letsencrypt-staging" "resource_namespace"="" "resource_version"="v1" 
E0914 17:36:03.548101       1 controller.go:163] cert-manager/controller/clusterissuers "msg"="re-queuing item due to error processing" "error"="context deadline exceeded" "key"="letsencrypt-staging" 
I0914 17:36:08.549436       1 setup.go:219] cert-manager/controller/clusterissuers "msg"="ACME server URL host and ACME private key registration host differ. Re-checking ACME account registration" "related_resource_kind"="Secret" "related_resource_name"="letsencrypt-staging" "related_resource_namespace"="cert-manager" "resource_kind"="ClusterIssuer" "resource_name"="letsencrypt-staging" "resource_namespace"="" "resource_version"="v1" 
E0914 17:36:18.550061       1 setup.go:259] cert-manager/controller/clusterissuers "msg"="failed to register an ACME account" "error"="context deadline exceeded" "related_resource_kind"="Secret" "related_resource_name"="letsencrypt-staging" "related_resource_namespace"="cert-manager" "resource_kind"="ClusterIssuer" "resource_name"="letsencrypt-staging" "resource_namespace"="" "resource_version"="v1" 
I0914 17:36:18.550114       1 conditions.go:95] Setting lastTransitionTime for Issuer "letsencrypt-staging" condition "Ready" to 2021-09-14 17:36:18.550108288 +0800 CST m=+166.489787378
E0914 17:36:18.550143       1 sync.go:60] cert-manager/controller/clusterissuers "msg"="error setting up issuer" "error"="context deadline exceeded" "resource_kind"="ClusterIssuer" "resource_name"="letsencrypt-staging" "resource_namespace"="" "resource_version"="v1" 
E0914 17:36:18.550260       1 controller.go:163] cert-manager/controller/clusterissuers "msg"="re-queuing item due to error processing" "error"="context deadline exceeded" "key"="letsencrypt-staging" 
I0914 17:36:28.551558       1 setup.go:219] cert-manager/controller/clusterissuers "msg"="ACME server URL host and ACME private key registration host differ. Re-checking ACME account registration" "related_resource_kind"="Secret" "related_resource_name"="letsencrypt-staging" "related_resource_namespace"="cert-manager" "resource_kind"="ClusterIssuer" "resource_name"="letsencrypt-staging" "resource_namespace"="" "resource_version"="v1" 

$ kubectl -n cert-manager logs -f cert-manager-cainjector-6ff65c66fd-z8tbw
I0915 10:48:50.725518       1 controller.go:178] cert-manager/secret/validatingwebhookconfiguration/generic-inject-reconciler "msg"="updated object" "resource_kind"="ValidatingWebhookConfiguration" "resource_name"="cert-manager-webhook" "resource_namespace"="" "resource_version"="v1" 
E0915 10:48:50.733174       1 controller.go:175] cert-manager/secret/validatingwebhookconfiguration/generic-inject-reconciler "msg"="unable to update target object with new CA data" "error"="Operation cannot be fulfilled on validatingwebhookconfigurations.admissionregistration.k8s.io \"cert-manager-webhook\": the object has been modified; please apply your changes to the latest version and try again" "resource_kind"="ValidatingWebhookConfiguration" "resource_name"="cert-manager-webhook" "resource_namespace"="" "resource_version"="v1" 
E0915 10:48:50.733316       1 controller.go:304] cert-manager/secret/validatingwebhookconfiguration/controller/controller-for-secret-validatingwebhookconfiguration "msg"="Reconciler error" "error"="Operation cannot be fulfilled on validatingwebhookconfigurations.admissionregistration.k8s.io \"cert-manager-webhook\": the object has been modified; please apply your changes to the latest version and try again" "name"="cert-manager-webhook" "namespace"="" 
I0915 10:48:50.736253       1 controller.go:178] cert-manager/secret/mutatingwebhookconfiguration/generic-inject-reconciler "msg"="updated object" "resource_kind"="MutatingWebhookConfiguration" "resource_name"="cert-manager-webhook" "resource_namespace"="" "resource_version"="v1" 
I0915 10:48:50.741147       1 controller.go:178] cert-manager/secret/validatingwebhookconfiguration/generic-inject-reconciler "msg"="updated object" "resource_kind"="ValidatingWebhookConfiguration" "resource_name"="cert-manager-webhook" "resource_namespace"="" "resource_version"="v1" 

$ kubectl -n cert-manager logs -f cert-manager-webhook-6984c6cbbc-zhwjw 
W0915 10:48:33.783799       1 client_config.go:615] Neither --kubeconfig nor --master was specified.  Using the inClusterConfig.  This might not work.
W0915 10:48:33.785307       1 client_config.go:615] Neither --kubeconfig nor --master was specified.  Using the inClusterConfig.  This might not work.
I0915 10:48:33.785502       1 webhook.go:70] cert-manager/webhook "msg"="using dynamic certificate generating using CA stored in Secret resource"  "secret_name"="cert-manager-webhook-ca" "secret_namespace"="cert-manager"
I0915 10:48:33.788419       1 server.go:138] cert-manager/webhook "msg"="listening for insecure healthz connections"  "address"=":6080"
I0915 10:48:33.788536       1 server.go:169] cert-manager/webhook "msg"="listening for secure connections"  "address"=":10250"
I0915 10:48:33.789029       1 server.go:201] cert-manager/webhook "msg"="registered pprof handlers"  
I0915 10:48:34.819424       1 dynamic_source.go:272] cert-manager/webhook "msg"="Updated serving TLS certificate" 

Anything else we need to know?:

cat staging-clusterissuer.yaml 
apiVersion: cert-manager.io/v1
kind: ClusterIssuer
metadata:
  name: letsencrypt-staging
spec:
  acme:
    # The ACME server URL
    server: https://acme-staging-v02.api.letsencrypt.org/directory
    # Email address used for ACME registration
    email: admin@example.com
    # Name of a secret used to store the ACME account private key
    privateKeySecretRef:
      name: letsencrypt-staging
    # Enable the HTTP-01 challenge provider
    solvers:
    - http01:
        ingress:
          class:  nginx

$ kubectl create -f staging-clusterissuer.yaml 
clusterissuer.cert-manager.io/letsencrypt-staging created

$ kubectl -n cert-manager describe clusterissuer letsencrypt-staging    
Name:         letsencrypt-staging
Namespace:    
Labels:       <none>
Annotations:  <none>
API Version:  cert-manager.io/v1
Kind:         ClusterIssuer
Metadata:
  Creation Timestamp:  2021-09-14T09:47:49Z
  Generation:          1
  Managed Fields:
    API Version:  cert-manager.io/v1
    Fields Type:  FieldsV1
    fieldsV1:
      f:spec:
        .:
        f:acme:
          .:
          f:email:
          f:privateKeySecretRef:
            .:
            f:name:
          f:server:
          f:solvers:
    Manager:         kubectl
    Operation:       Update
    Time:            2021-09-14T09:47:49Z
  Resource Version:  270254
  Self Link:         /apis/cert-manager.io/v1/clusterissuers/letsencrypt-staging
  UID:               dcb7e1b4-145e-4a3f-9bca-d663738699c9
Spec:
  Acme:
    Email:            admin@example.com
    Preferred Chain:  
    Private Key Secret Ref:
      Name:  letsencrypt-staging
    Server:  https://acme-staging-v02.api.letsencrypt.org/directory
    Solvers:
      http01:
        Ingress:
          Class:  nginx
Events:
  Type     Reason         Age                  From          Message
  ----     ------         ----                 ----          -------
  Warning  ErrInitIssuer  83s (x7 over 7m38s)  cert-manager  Error initializing issuer: context deadline exceeded

Environment details::

• Kubernetes version: v1.18.18
• cert-manager version: 1.5.3
• Install method: static manifests

/kind bug