Yeah this is the worst thing about STO in my book right now. Whenever you change from TAC to ENG setup for example you always have to mess around that annoying power tray and move abilities around. Very annoying.
i think I've figured out PART of the problem... When you bind a key to the slot "skill 1, row 1" it seems to bind to the OBJECT in that slot. So when you swap out weapons -- guess what? Maybe the weapon drops inot that same skill1/row1 if you're lucky, but now your mapped key doesn't work!!
I've noticed this twice so far. Not sure what goes on with my key bind setup, but they stop working even if something new is in that slot.