Yeah, the trainer seems to disable the achievements if that is what you mean, Alefe. The cheats themselves do still work though.
It's not an issue with the trainer, if you read the steam forum, you'll see that it's an error on the devs side, no one can get achievements until they resolve the issue; it sees all game sessions as modified/checks for the wrong checksum.
Anyway, the default trainer hotkeys interfer with the game, F1 though F10 are used by default and cannot be rebound ingame, as is numbers 1 though 0. Numkeys are fine though, but that means you have to manually rebind the trainer keys every time you use it, since it doesn't save the changes.
As others have stated, Trait Points and Perks, as well as Edicts do not currently work, just gives an error message.
In any case, MrAntifun, you might want to wait with publishing an update for the trainer, until later this week, when it's updated with the achievement fix, in case the updated game causes issues with the trainer.