I am experiencing the same thing: the barracks mod options do not work. I have followed all the steps outlined in previous posts.
Interestingly, my AV (Norton) is giving me a block notification when I launch the trainer, but the trainer launches and gives every appearance of operating (except these options don't work). All of the directories cited above, and a few more, are on the ignore list. I have no idea how to make it leave the trainer alone. Can anybody offer some insight? This is extremely annoying.
www.cheathappens.com/norton_antivirus_troubleshooting.asp