The situation went something like this:
"Mr. Brassfield, why are we not firing beams?"
"I don't know Captain, we should be able to manual fire. [click] We're within knife-fighting range, [click] and beams are charged, [click] but nothing's happening. [click] Screw it, switching to Auto Beams [click]"
*pew pew*
"Much better Mr. Brassfield"
I was running two instances of the game, the server and my Weps seat, with the server being displayed on a projector connected to my laptop. We had 3 other players, Engie, Sci+Coms, and Helm+Cap'n. We're thinking the problem may have been because the server computer was also running a game instance, but I have a fairly powerful laptop (Asus G73), so resources should be a non-issue. To compound on the mystery, I ran a "solo" game as all the seats to familiarize myself with what my crewmates see (two instances again, server+game, me at all 5 seats), and I had no problem using jump drives or manual beams.
To eliminate variables, next time we play we're going to run the server on a dedicated computer.
-Weapons Master of the nascent U.S.S. Titan, proudly calling Moriarty, NM her home.