Just wanted to chime in that I too am having this issue.
I'm playing as the Fringe. I'm level 36.
Superior Raider Bay II
Ship Level: 40
Ship Max Count: 4
Energy Required: 221
I have more than enough energy. When I right-click or press the number key to launch nothing happens - same situation as ebarstad. One quick added note - this happened during a multiplayer game, so I gave the bay to a friend who had a lower level ship than mine - it worked fine for him.
Any ideas, Shadow?