when your trains move between navius and underground, new train entries are generated in The FAT controller. and after some time, at the next train movement:
debug->Update->Trains: = 10.918/0.003/1093.467,
which gives a frieze of about a second each time each train moves.
I propose to add this mod to the incompatibility list.

I would have to look at, I have never used Fat controller though but it sound like it's not incompatible it's just not great.
Marking mods as incompatible is a last resort.

I have removed The FAT Controller mod. a standard train manager is quite enough