i think something did break last patch as the powers tray in space jumps about between instances. the only way i could properly rearrange the tray when i got my new ship was to minimise it to a single row and use the updown arrows to move it to row 2 and 3. I could then add skills to all the boxes. After that i restored it to my preferred 3 rows showing option and locked it.
Make sure the "Lock Tray" checkbox at the bottom-left of the powers window (P) is not checked.
If you remove a power from your tray by right-clicking and dragging it away from the tray, you will be unable to put ANYTHING into that slot on ANY of the numbered rows until you go through a loading screen. In addition, if you try to put something there after you've removed a power, it'll empty out that slot on every row.