My bad, I'm not explaining it correctly. The switches aren't the issue as far as I can tell. The window always goes down. Sometimes, while using either door switch the window will not go up, other times it will. When it fails to go up, it does move an inch or two before stopping. At this point you have to go back down before it will be able to go up again (and stop at the same point). I think this is the "pinch protection" feature. It detects a load and thinks something is blocking the path so it cuts off.
Lifting and lowering the window manually in its track there is a bit of resistance but its not gritty or anything like something is in the track. I found from searching around that when using the key in the lock cylinder to roll up or down windows the "pinch protection" is disabled. This allows the motor to power through whatever obstacle seems to be stopping it the rest of the time.
My conclusion is that the track (either at the window edges, or where the window clip glides) is a bit warped or not lubed well or something. Since it doesn't stop all the time I think this resistance is fairly close to the threshold allowed by the "pinch protection". Since the key lock trick is a reliable workaround and its just one rear window, I'm fine with it. It does seem to work reliably when rolling it up and down halfway or so. It only gets dicey near the bottom of its travel.
EDIT: One possibility I just thought of is that the sheetmetal insert got warped a bit during removal. That gasket is damn sticky

Maybe the cable pulleys and coil aren't quite lined up as nicely as they should be?