My experience from last December sounded exactly like yours. I was flying LAX-SFO-HKG on a W fare upgraded with a SWU. Upon completing online check-in, my seat assignment went to "---" as well. I confirmed with the phone agent that it is indeed a glitch (a website display issue). I ended up flying the seat assignment I reserved and everything was fine. So, I don't anticipate any problems for you either.

Enjoy the trip!