I have the same problem on both of my Klingon toons, sometimes the power tray abilities DO NOT let me click them. I'm not talking about the misfire thing, They just don't work. but when i use the keyboard to fire off these powers, or click the same power on on the BOff tray, it works fine.this problem comes & goes, but it's killing me. I fly with WASD & fire powers/look around with my mouse. having to double check my tray every time i use a power, then drop my mouse in the middle of a fight & look at the keyboard to find the appropriate key, then get my mouse again has made PVP pretty much undoable to me. by the time i get all that done, I'm either dead or irrelevant, hopelessly out of position to alpha. It's flat out un-fun & frustrating. My Fed, however, seem to work just fine.
This happens to my fed main ALL the time. My theory is that it's a lag issue. My record is having to press something three times before it worked. I don't think it's happened at all for my klink, but I've only started to PvP with him when he hit commander, and he's currently Cap2. I haven't PvP'ed with my boring Fed Eng alt yet, so who knows if it will happen to him. If my lag theory is correct, I imagine it will. Considering it seems to happen the most in CnH's, lag seems like a good theory to me (I don't think I've even done a CnH with my klink yet - only Arenas seemed to pop at Commander level).