I'm happy to read you still managed to finish up even with the faction bug in effect. It must have been somewhat annoying for you.
I am going to ask what may amount to obvious, stupid questions, but yet in an attempt to isolate the cause, here goes:
Where are you dispatching your henchmen, in the Reaper Realm or elsewhere? If "elsewhere", where exactly?
Do you always dispatch one before asking another to join? (I am assuming your party is full with 2 pals, in this case)
Is there any chance you may have injured a neutral NPC along the way? (This includes rats, pilgrims, quarry workers, etc.)
Is Chapter 3 the only module where you experienced the henchman faction bug?
I've read a lot about the factions changing in the legacy forum but never have figured out the actual source(s). It would be very handy to compile a list of these causes so others could avoid them and enjoy the game from beginning to end.