jsign: Signing certain MSI files corrupts them

Hi, My team has encountered an issue while using the programmatic API to sign some MSI files. We sign many files every day including other MSIs and have no issues with the vast majority. We’re not sure why these couple of MSIs are the exception. The signing doesn’t fail or throw any errors at all but immediately after the MSI is signed it becomes corrupt and attempting to run the MSI displays the following error:

The code we’re using to sign is as follows:

KeyStore keystore;
AuthenticodeSigner signer;
Signable file;
File certFile = null;

try {
	certFile = new File(certFilePath);
	keystore = KeyStoreUtils.load(certFile, "PKCS12", certPassphrase, null);
	
	signer = new AuthenticodeSigner(keystore, certKeystore, certPassphrase);

	File[] filesToSign = listFiles(regex);
	
	for(File targetFile : filesToSign) {		
		signer.withTimestamping(true)
			.withDigestAlgorithm(DigestAlgorithm.SHA256)
			.withSignaturesReplaced(true)
			.withTimestampingMode(TimestampingMode.RFC3161)
		       .withTimestampingAuthority(timestampURL);

		file = Signable.of(targetFile);
		
		signer.sign(file);				
	}
} catch (Exception e) {
	// ...
}

It’s pretty straightforward so I’m not sure what’s going on or additional spots to look.