Whenever I launch plutonium, my pc resolution changes, and I can't turn it up in any of the games.

[deanial]

Problem in title, only started happening after I installed T6 for black ops 2.

[Resxt]

Try this

Go in the bootstrapper command prompt (the console opened when you start the game)
and paste this (right click) r_fullscreen 2; vid_restart then press Enter