I've noticed powers not activating if I click on them to quickly in close succession when in my BOP. I think some take a little longer to activate than others. Most notable when coming out of cloak and buffing up for an alpha strike.
One day I'll get my tiny brain around key bind syntax, probably the best way to go about it since I normally use the same uncloak, alpha pattern, delta pattern, shields subsystem, rapid fire and tactical team on each attack run or the AOE versions if faced with a group of ships. Apparently you can put in slight pauses between activations which would probably solve the problem.
I think the UI lag in general is getting worse. When i go to ESD the menu lag makes gearing and moving stuff around nearly impossible. I see input lag on all classes of ships, from both sides, K+F. Also, it seems some skills take longer to activate than others and some lock you out from using another skill while they are being activated.
Lets hope Cryptic can get ahead of the F2P lag soon.