Did you load up the file in CM 2.01, saved after the replay in the command phase, loaded the file in the new version and processed your turn? This should do the trick.
BTW is your latest file you send me 2.01 or 2.10? If the newer version is it done the way I described? Otherwise there will be problems. If it is in the old version should I "update" it to 2.10? I got both versions installed and can do it...