Would this area have something to do with this....
New Message Autoresponse
Confirmation sent to user when a new message is appended to an existing ticket. (Email and online replies)
In the templates?
I have this set like this for the subject...
VooDoo DESIGNS Support Ticket #%ticket Updated
Should I leave it the default and if so what was it?
Like right now i just did a reply to one... It removed it from my inbox but created a whole new ticket for it with this subject:
Subject: RE: VOODOO DESIGNS TICKET #631116 HAS BEEN UPDATED