OK, gave your described process a try....found an email in one of my smart folders on the Mac, drafted a reply and sent it on its' way back to the originator.....NO spurious copy of said outgoing message appeared in my Inbox, just in the Sent box (as expected for normal handling).
When I then Forwarded that message from my .mac Sent folder to my .gmail account, I received it in my Inbox as expected AND got an additional copy of the same email in threaded format in my Gmail's Archive folder.....this behavior is normal for Gmail as it retains an Archive copy of EVERYTHING.
I looked through the Mail preferences and View options to see if there might be a setting that would create the same symptoms as you are experiencing, but didn't see anything that looked like it was even close.
This is sounding more and more like it may be a Gmail-specific issue with your account....have you looked through the forums/FAQ's at Google to see if there might be any similar issues already on-file or resolved?
