When you decrypted from the command line, did you notice the plaintext blob preceding the HTML message content? Look for "Content-Type: text/plain;" and see if there is an unmodified verification URL there.
You might have only noticed the HTML one, which will be a pain to cut & paste. If it's still broken, please contact me.
Incidentally, I've been using both GPGTools/Mail.app and Gmail/Mailvelope without trouble. The latter doesn't open clicked links in a new tab, though. I've had to "Copy as" and paste in another tab.