argo-cd: AutoSync doesn't work anymore

Describe the bug

When I change my bootstrap-application in git it doesn’t get synced anymore to kuberntes, although AutoSync in argocd is enabled. Only when I click ‘Refresh’ in argocd webconsole, the application gets OutOfSync and Sync process starts.

To Reproduce

1. change something in the git-repo of my bootstrap-application
2. wait the AutoSync interval of 3 minutes, nothing happens (also waited for an hour)
3. clicked ‘refresh’ in the webconsole of argocd for this application
4. application gets OutOfSync and starts synchronization process

Example

I am not able to create an example, because it is vey specific to our environment. However, maybe I can narrow down to a basic example. Right now I do not know if that happens with every application in our environment or just with our boostrap-application.

Expected behavior

AutoSync should sync the application without any user interaction.

Screenshots

Version

1.2.0

Logs

logs from application-controller, when git-repo and kubernetes is already out-of-sync, but argocd doesn’t recognize it (since we have lots of applications defined, I tried to filter a little bit for the bootstrap-application):

time="2019-09-22T09:41:12Z" level=info msg="Refreshing app status (controller refresh requested), level (1)" application=bootstrap-application
W0922 09:41:12.393879       1 listers.go:77] can not retrieve list of objects using index : Index with name namespace does not exist
time="2019-09-22T09:41:12Z" level=info msg="Comparing app state (cluster: https://kubernetes.default.svc, namespace: argocd)" application=bootstrap-application
time="2019-09-22T09:41:12Z" level=info msg="Skipping auto-sync: application status is Synced" application=bootstrap-application
time="2019-09-22T09:41:12Z" level=info msg="Update successful" application=bootstrap-application
time="2019-09-22T09:41:12Z" level=info msg="Reconciliation completed" application=bootstrap-application fields.level=1 time_ms=281.376147
time="2019-09-22T09:41:12Z" level=info msg="Refreshing app status (controller refresh requested), level (1)" application=bootstrap-application
W0922 09:41:12.674738       1 listers.go:77] can not retrieve list of objects using index : Index with name namespace does not exist
time="2019-09-22T09:41:12Z" level=info msg="Comparing app state (cluster: https://kubernetes.default.svc, namespace: argocd)" application=bootstrap-application
time="2019-09-22T09:41:12Z" level=info msg="Skipping auto-sync: application status is Synced" application=bootstrap-application
time="2019-09-22T09:41:12Z" level=info msg="Update successful" application=bootstrap-application
time="2019-09-22T09:41:12Z" level=info msg="Reconciliation completed" application=bootstrap-application fields.level=1 t

log when I click Refresh:

time="2019-09-22T09:43:57Z" level=info msg="Comparing app state (cluster: https://kubernetes.default.svc, namespace: argocd)" application=bootstrap-application
time="2019-09-22T09:43:57Z" level=info msg="copying credentials" credUrl="https://gitlab.e-bk.m086/" repoURL="https://gitlab.e-bk.m086/arz-container-plattform/k8s-platform.git"
time="2019-09-22T09:43:58Z" level=info msg="Initiated automated sync to 'd1ac81ea342f68997be69ff2befbf2b0ec1b045f'" application=bootstrap-application dest-namespace=argocd dest-server="https://kubernetes.default.svc" reason=OperationStarted type=Normal
time="2019-09-22T09:43:58Z" level=info msg="Initiated automated sync to 'd1ac81ea342f68997be69ff2befbf2b0ec1b045f'" application=bootstrap-application
time="2019-09-22T09:43:58Z" level=info msg="Updated sync status: Synced -> OutOfSync" application=bootstrap-application dest-namespace=argocd dest-server="https://kubernetes.default.svc" reason=ResourceUpdated type=Normal
time="2019-09-22T09:43:58Z" level=info msg="updated 'bootstrap-application' operation (phase: Running)"
time="2019-09-22T09:43:58Z" level=info msg="Initialized new operation: {&SyncOperation{Revision:d1ac81ea342f68997be69ff2befbf2b0ec1b045f,Prune:true,DryRun:false,SyncStrategy:nil,Resources:[],Source:nil,Manifests:[],}}" application=bootstrap-application
time="2019-09-22T09:43:58Z" level=info msg="Comparing app state (cluster: https://kubernetes.default.svc, namespace: argocd)" application=bootstrap-application
time="2019-09-22T09:43:58Z" level=info msg="copying credentials" credUrl="https://gitlab.e-bk.m086/" repoURL="https://gitlab.e-bk.m086/arz-container-plattform/k8s-platform.git"
time="2019-09-22T09:43:58Z" level=info msg="Update successful" application=bootstrap-application