Well, this is based on memory with all its inherent inaccuracy, but when I first played Freespace2 with a joystick (Win98) I had trouble with aiming, I was constantly overshooting what I was targeting. Practise over time reduced the issue, but I noticed it again when I played something like XWA and returned to Freespace2.. However, I now play on Linux and I don't believe I have the same problem. I'm also currently playing XWA under wine and I'm not having the "readjustment" issues from switching between the two that I recall from before.
I believe this is significant because (AFAIK) Linux uses SDL for input and Windows doesn't, so maybe there is something odd in the Windows joystick code?