I am seeing the same behavior with the default templates. The issue does seem to relate to the Subject of the template as I have found that if I get rid of everything except [TITLE] Ticket= [TICKET_NUMBER], I can reply to email notifications without errors. I did try your suggestion but so far I still see get the error.
I opened a request with BMC about this and it is a known issue. I was told that a hotfix is in the works for this and should be out soon. I tried to remove the period too and got the error. We had tried sending the email various ways and haven't got any to work yet for us. I'll take a look again at some of your suggestions and let you know if they work for me.