As for why exactly it's happening, I can't say that I immediately know by just looking at the symptoms.
It's on our radar to review and find a fix for. Until then, beware of Boarding Parties. (Honestly never thought I'd say that...)
That's good news Bort because people in PvP today were talking about not bothering anymore and calling this guy names I can't repeat. i apologised to him for accusing him of hacking but it seemed so extreme and was very like the ET bug recently fixed that put all your timers on CD for 2 min IIRC. Sooner it's sorted the better, or at least make TT available and able to clear it.