sorry to hear, this bug is plaguing PR as well. Since I first ran into it, I've been investigating it and trying to find a way to avoid its occurrence. My guess is, that every unit, no matter if it is a single unit or part of a squad/squadron and no matter how it enters a tactical battle gets stored in a table, which cummulates with every battle and when a certain amount is reached, a threshold overflows. With the mentioned results. That applies not only to mods but the vanilla games, too. EaW (as I've been told) and FoC (as I have been provided with evidential savegames from our community).
After trying countless things (I even went into the savegames with a hex-editor for investigation), I came to the conclusion, that it cannot be solved by our modders means. So I turned to Petroglyph, told them my findings, my assumptions and sent them some corrupted savegames. The fact is, the issue is known to them. The good news is, they would be willing to take another look into it and if an easy fix is possible, they would bring out another (small) patch. Well, regrettably when there're good news, there always have to be bad ones. Petroglyph claims, they cannot act by themselves. They have to coordinate they efforts with LucasArts (probably, at first they need their permission). Petro warned me, that working with LucasArts might be a slow process at the moment... Therefore, the next logical step was to write to LucasArts. Well, I know now, what was meant with "slow process". I can tell you, it wasn't just slow, it was painful. Very painful. I was even close of giving it a rest, but after 10 mails or so, they told me, they could not promise me anything but they would give my request a review.
At every opportunity, I encourage people to write to them, show them, that there still is the desire to get at least that bug fixed. And now that I see, you're also troubled by that issue, I'd like you to come aboard. Let us pestering Petroglyph and especially LucasArts with even more voices!