Note the issue with steam is that XCOM: Enemy Within/Unknown uses an Anti-Cheating system what nulls any abnormal or incorrect commands, I.E most of the money cheats and resource cheats, seeming as they are technically in words classified as a quest reward. Try turning steam offline, and then see, because then XCOM: Enemy Within/Unknown can't send data to online servers to reset any abnormal scripted commands. This is not a guaranteed fix, as I have not had time to try it myself, as I am in university, but you should defiantly see if it works. ^_^
Technically there is no way around this, though it can be done obviously, (As saying things are impossible is unethical) the new update probably strengthened this, so you will have much more trouble.
May I suggest you use a Hex Coder instead, as I love to be lazy and get a trainer, this game seems to make things other than money, scientists and whatnot easy. Though I feel many more games need the anti-cheat system, but once you have completed the game, and you want to mess around it's nice to be able to cheat, or if you are like me, you just say debugging. Haha.
Though I must agree the problems are annoying, I would probably have to say to MrAntiFun that you might want to put somewhere in this description that you might want go offline on steam first if it works, that's IF. But I am only putting up a possible reason as to why, I might not be right.
PS: I love your Trainers MrAntiFun, though I feel sorry for you because of the high demands... (It would annoy me. Hah.)