Strange tire problem with LX rim

I always install and pump up tires on my Strida with the bike lying down, so the wheel is horizontal and no weight acting on the tire. Then when there is a tiny bit of air in (say 10psi) I check the tire is as even as possible (its rare for it to be perfect), then pump up more until its full.

Then for normal pump-ups the bike can be left standing up (unless the tire is completely flat again).