No, I have this issue too. Only some squares. A bit of wierd clicking around and stuff and sometimes I can reset it.
Basically, when moving it deletes it in the old place, but doesn't create it in the new place. It might be related to ship upgrades as this is when I've noticed it (then again, that's really the only time I start shuffling skills too.)
I have this problem, zoning works for a moment. Zoning to where there are few to no other players works better. Hitting escape, then options, then video and setting the lazy bar to lowest graphics setting works best.
Edited to add: You can always turn your graphics back up when you get done sorting your powers tray.