Anyone noticing that you can't get achievements with the trainers on? Is that a new trend or something?
Steams "unofficial" policy is that of not caring what you do to your single-player game as long as you don't affect any leaderboards. The topic of trainers has come up a couple times and the general consensus is that they have better things to worry about.
What game are you having issues with? Maybe someone else has it and can tell you if they got achievements.
I have recently unlocked achievements in Test Drive Unlimited 2, Red Faction Armageddon, and Fallout New Vegas, all with trainers running.