There is absolutely no code that could cause this issue. Probably a addon do cause it. The A-CEP is quite a long time "in the wild" so such a serious issue would have been reported shortly after release.
A-CEP does spawn AI, it controls them as far as it generates wayponts and keep them (hopefully) moving. It also controls unit caching. Thats basically all it does. Nowhere is any code that could be able to cause such behaviour as you describe it.
Start your ArmA without any addons (and i do mean absolutely no addons), remove all non A-CEP scripts you use and then see if the error still exists.
If it does (which i strongly doubt), please send me a copy of the mission (zip the working folder, don't even think of sending it pbo'ed). and i'll have a look into it.