To clarify, I think the issue is that Indy top bushing seats are sort of oval-shaped instead of round, which might provide some benefit, but also has the side-effect of sometimes letting the hanger end up stuck off-center. Also, I don't mean that the trucks are leaned (as when turning), I mean that the hanger slides sideways (still perpendicular) so that the top bushing is jammed up against one side of the wider oval bushing seat (not centered).
My pivot cups are ok. This issue happens even with brand-new Indys.
Do you always hit curbs or do certain tricks to one side?
I think something like this might be due to constant motion in one direction, eg always doing backside slappies tends to push the trucks hard on an angle and could push the bushings in a certain direction too.
If you mark the bushings, then rotate them a quarter turn, or half turn, does the board still do the same thing?
When you look at the bushings, if they have oval holes rather than round holes where they sit on the kingpin, I think it would definitely be something to do with how you are skating, but I would never rule anything out.
Pics would be really good to see too, as sometimes it is harder to get it right with a mental picture and a lot easier with a physical one.