EAW 101 :

Most likely not a mod issue. You should always create a new save file when saving i.e. creating many save files, and not save during battles or close to cycle start/end, but even so you *may* sooner or later get a corrupted save file no matter what as there are some rare base game issues as well e.g. suspected save corruptions when too many ships are in hyperspace or if a hero recently died. But as long as you have many save files there should hopefully be one not too old that still can be loaded.