Also having the same problem, I have gained no reputation after a specified point in the game (not sure where that point is exactly). Eder, xoti, serefen, aloth all have a positive reputation of 2, but no other companions have gained anything. I believe it started once I chose to be in a relationship with Xoti.
***update*** I have been playing more and monitoring my reputation. I noticed that actually I am not gaining any reputation of any kind, faction included.