I had the same leveling problem with 0.903 or 0.960, and at that time I also had deserter party with only my player character in it. Turned out it's a problem with missing a few lines so some dialog lines or indices messed up or something.
Now I have the same problem with 1.010 when changing things around. Yes, I can workaround the problem like someone did in this thread, but that would just hide the true problem elsewhere.
Got to review all my changes now...
EDIT: I found my problem. After adding companions, I forgot (again, like last time) to change this line in initialize_npc:
(store_mul, ":string_addition", ":slot_addition", 16),