Every few minutes of playing in Freespace, my controls will freeze but the gameplay will continue. After a few seconds it gets better but it is very irritating because I fail missions a lot when I ram my ship into something.

Freespace 1 or 2? are you in XP, Vista, or 7? Are you using Freespace Open?

That's not normal behavior :)

Freespace 1 with no mods and I am in 64 bit Vista.

As one might expect, I have indeed heard that Freespace 1 has more compatibility issues than its sequel. Unfortunately I cannot really help you with your setup. I could suggest the usual things: run as administrator/in XP compatibility mode but I don't know if that would really help. If no one else solves your problem, you can try Freespace Source Code Project and playing Freespace 1 via FSport. That's what I played. You essentially get to run an old game in a modern game engine.

Best of luck.