This occurs after I map the joystick as prompted before registering. It's a Boom! PSJoy converter box for a Dualshock 2, and it uses DirectInput. I've so far tried setting the joystick type in the DOSBox conf file manually, and I've also tried turning "timed" off and on (it needed to be on for Wing Commander.)

I'm told the mouse controls work basically the same as the Freespace series, which I quite enjoyed, so I can play without the controller, but I'd like to try it. Has anyone else had this problem?

Yes I get this with my 360 controller in the 98 version. The 93 I just use my mouse like I used to play it, though I will get certain spots where it will bounce around away from where I want it, but I'm using a crappy mouse at a friend's house, I'll have to test this out with a good one when I get home.

Any help on the 360 drifting would be great, yes it is calibrated.