We are playing a game, and while I haven't had any problems, my mate lost all of his infantry in the beginning of the game. We are playing the Blenheim Blunder, he is British. Also he just said that he unloaded a truck, which made infantry sounds, and he got a tank, which cannot move.
There has been a lot of discussion of this, and I have been experiencing it as well. It appears to be due to the VCR replay. It also only seems to affect certain OOBs. If you playing unsecure games, you can simply make a copy of the files, save them with a differnet number, Save000.cnt as Save009.cnt for example, then use the VCR on the copy to see what happened. Then your actual game will be unaffected. I don't think the secure games will allow this however.
So, don't use the replay in secure games, and always save a copy if you do. I would think you could re-unzip the files after viewing the replay and then go from there.