In case the problem persists, could you send a screenshot of Mail.app > Preferences > GPG Mail.
Could you send us an unencrypted and unsigend test email to team AT gpgtools DOT org to which we respond with an unencrypted and unsiged msg to which you then respond so we can check what happens when you reply to a message.
Is the behavior you are seeing 100% reproducible or is it more like some accidental behavior happening unfrequently?
Are you seeing any SMTP (mail server) issues when trying to send your messages or while you are working on drafts?
Do you have additional mail plugins installed besides GPG Mail?
All the best,
Disclaimer: This is a development version which has not been thoroughly tested yet - bugs or crashes are to be expected. Thanks for helping us test.