Well I've tried a variety of things trying to fix this. Reinstalling NanoFX and Foundation have not worked. I've tried using the Quickbattle.py from the KM mod, since the problem doesn't seem to manifest there, but that also didn't work. All I can say is that MVAM Infinite is definitely the cause and red alert only works properly when MVAM is disabled.
Edit: There wouldn't happen to be another file that affects red alert, would there?