Thanks for the reply, Greenfist.
I am running mods, and in fact I thought it might be TPW, as it messes with animation speeds. But I deactivate this mod to play Whole Lotta Altis, and the effect is still present.
I just tested in the editor with just a squad, and after about 5 seconds running, all squad members started to move at 1/2 the speed, which might be due to the fatigue. If it's the case, the fatigue applies waaay too early.
I have seen 1/10 animation speeds (aprox.) playing without TPW in some squad members. It might be related to the fatigue system. Is there a way to deactivate fatigue, or a mod that does it, so to test if it's this system the cause?
[EDIT 1]: By the way, this only affects AI, the player remains unaffected...
[EDIT 2]: It seems it might be caused by TPW or CBA. Deactivated both and went to play with the editor. I haven't been able to reproduce the problem since then. I'm going to search what might be causing it.