I'm also having the same problem, just reinstalled the game to play it through again. Now, when I select what I want to modify on the trainer, I hear "activated", but when I try to add or subtract, I hear "deactivated" before "activated", and nothing happens. Guess the trainer needs another update. Anyone know if they still plan on doing so?
What expansion are you talking about? The 'Second Wave' options have been available in the game since launch, you just had to modify a file to get them in. All they did was re-enable them. I wouldn't call that an expansion. The only expansion to this game hasn't been released yet: Enemy Within.
I just got through playing for about 4 hours on a currently updated XCOM, and the trainer works perfectly fine. Are you sure you're following the instructions properly? One of the recent updates to XCOM made it so you have to jump through hoops to get it to work properly, but I promise you it still does. I've been able to modify all stats, both on and off the battle field. I haven't messed with gold, because I use cheat engine to hack that. I think adding too many engineers/scientists too early in the game sort of kills the length of enjoyment of the game, so I don't mess with that, either.