Karsten,
It took me awhile to correlate seat movement problems with annual disassembly and re-assembly. The shop we use now is tremendously good with Comanche stuff but everyone does make mistakes .... thanks to Clifton, haven't had the rail problems for years. It could be the rollers but you might also check the items below.
The 39 I have has had seat movement problems in the past - #1 cause has been the seat rails were improperly installed - rails are each subtly different but they are different and it does matter where they are placed in the cabin. It wasn't that the seats wouldn't move, it was just difficult. I have now permanent marker labelled them on the bottom to reduce future bad installs.
Second most common problem has been carpet binding. There are 'holy wars' on whether rails should be on top or next to the carpet rails. Piper had them on top so ours have always been there. Sounds like you have already ruled this out but just in case. Carpet thickness is much greater than the original carpet.
In general, I've learned the hard way to post-annual the interior to make sure I have unimpeded, easy access and operations of/to sump drains, fuel selectors, emergency gear area, fuses, seatbelts, seats, doors and that seat rail end protectors get back on. I smile at that last one because of the memory of my Mom when she still owned the plane inadvertently dropped her Diet Coke can as she got in the Twin. She carried it until she was an hour out from landing and then drank it. Of course as it fell, it hit the edge of an unprotected seat sail end and it poked a tiny, tiny hole. The resulting spray was funny to watch us scramble to stop it. She had visited us in TX and was flying back to Chicago - we got her another can as we thought it would be hard to fly with one finger strategically placed on the can hole
for 5 hours.
Hope something here helps. Happy New Year!