My first guess would be fuel consumption. Possibly the cars are running out of fuel at the beginning of the pit stop window and hence come both to overcome a possible DNF. Try reducing AI fuel consumption on a track where this happens regularly and see if this fixes the issue. If so, you know where to start. I'm not playing with this mod, though, so it's just a shot in the dark.
GPGSL : Team Owner of 'Maverick Track Performance' (MTP)