First off, I know that this isn't technically a Linux game or a Linux board but I know enough people here do use this game with WINE so I thought I'd try asking here first since it would be the best place (I hope).

My problem is that randomly the left mouse button will click in game for no reason. I've left the computer alone to see if it does happen and it wasn't me clicking something by accident. I've done it with both my mouse plugged in and with it plugged out (I'm using a laptop) so its not something wrong with my mouse. I'm running Linux Mint 12 and have the latest version of WINE installed (this problem has shown in both Gnome and KDE). I've done a Google search and nothing has come up. Also, this doesn't happen in anything else that I know of (no other game, program, ect...)

This is a big enough issue to make the game unplayable since I've been in the middle of a fight and then suddenly the guy just says "All right" and walks away, causing him to get hit since he stopped fighting. Thank you for any and all help.

Out if curiosity, did you figure it out? I've played it on Linux too, at least part of it, and never had such a problem. Nothing came out from a quick search on the interwebz either.

No, the problem is still there. The game is still unplayable.
I've tried running the game on both Gnome and KDE (to see if it was a problem with a default program, like KDE's auto-mouse click program. Even uninstalled that to see if it would help). Launched both the short cut created by the GoG installer and the program file itself to see if it was a problem with the shortcuts extra instructions. I'm running it on Linux Mint 12 and did a Google search but wasn't able to find anything (mostly find posts about either Linux Mint, WINE or Planescape Torment so wasn't able to really find much). I have the latest version of Wine (add the PPA to my package manager). I also made sure the let the Installer check the file to make sure it wasn't a bad download.
Whats worse is its starting to get worse. Now it sometimes opens the Menu for saving the game, ect... (when I try something new I launch the game, it takes a few minutes but always happens). I'm out of options and have just reached the point that I've given up on the game. I look here to see if anyone has any remote ideas but nothing.

http://appdb.winehq.org/objectManager.php?sClass=application&iId=294

That may be of use. Are you able to try another distro?

I've searched on the internet for days when I tried to install it on WINE, because I wanted to play it on fullscreen as intended, but I don't remember ever seeing your particular problem. Which doesn't mean no one else had it, just that it's probably rare. Maybe post your WINE config, what settings are you using, what additional libraries, things like that. Also weidu log.
Does the console say anything? Specially when the game is starting, it might get flooded with errors once you start playing. Did you try setting the windows version to NT 4 or 3.1? Wine complains about that at some point. Did you try playing with the "automatically capture mouse" setting? Do you have winetricks? Do you maybe have dinput.dll set in WINE? It causes trouble. If you don't have it, maybe try installing it, use winetricks for that. Did you try running the game in a fresh WINEPREFIX?
FWIW, http://www.gog.com/en/forum/planescape_torment/planescape_on_linux_wine_howto. That's how I installed it, maybe you can find some hints there.
Also, my advice, play it on Windows if you can. In Virtualbox or something, it's a way better experience, at least my install would slow to a crawl when there was a lot of text from damage flying around on the screen. But I did play a good chunk of it on Linux, alternating between OSes.
I'll say it again, because it's important. Use a fresh WINEPREFIX if you aren't already.