Switching primary and secondary mouse buttons problem in some games

I play games left handed and so I enabled the "switch primary and secondary mouse buttons" option in windows. For most games this works fine, but ocasionally I play a game that won't accept that I've switched my mouse buttons. Obviously I can rebind the keys but its still very annoying that in every menu/ingame action aside from shooting I can't click the options with my index finger. I have had this problem in windows XP, Vista, and Vista 64 (which I am running now).

I was wondering 2 things:
-Is it possible to switch the mouse buttons on a hardware level or somewhere else that will make this take effect in all games?
-With mice that you can load hardware profiles on (like the razor diamondback), is it possible to switch the buttons on the hardware so it take effect in all games?

Games primary/secondary mouse button switch works on:
World in Conflict, Call of Duty 4, all Half life 2 & HL1 games, WC3, WoW, most other games I've played over the years

Games primary/secondary mouse button switching doesn't work on:
Bioshock, STALKER

Thanks for the help