JIRA is not able to detect the new PKCS signature file's content type (as the content type has been changed from "application/x-pkcs7-signature" to "application/pkcs7-signature") in the email that is fetched from POP, hence the file will be added as an attachment in the issue instead.

Old content type: application/x-pkcs7-signature
New content type: application/pkcs7-signature

Please see the RPC: http://www.rfc-editor.org/rfc/rfc2311.txt