Over the past 2 weeks I must have shot over 1000 shots with a D1X and the SB80DX both indoors and outdoors. I used mostly DTTL Matrix and I did find that the shots not exactly perfect as to exposure with this setup. I could be over on one shot, under for the next and then perfect for the next. Same place, same people and on tripod. I made sure the flash was back up each time. My F100 with the same setup always was perfect.
I believe the problem is with DTTL. There isn't a film plane to read the exposure on the digital camera so the flash sends out a pre-flash to figure out the flash reading and sometimes will missread the exposure. Using open shade without flash the camera knows what to do, but with flash it's guessing. One stop either way isn't bad. That can be fixed, but anything over that and using a JPEG setting could be trouble when fixing these shots.
I'm still learning and there's a lot of experience in these forums.