I am unfamiliar with most of what you just said, sadly enough, but I am running it off wine because I have a Mac. I also don't have a numpad keyboard, which is why I am trying to play it with a mouse. Runs great, but the mouse just jumps all over the place. I suppose I could spend the time remapping all of the keys, but I thought I'd give this a shot.
I'm running it on a good old Microsoft USB mouse from way-back-when.
Actually I run it on a Mac too - may I suggest using Freespace Open? Volition (the developers of Freespace) released the source code to Freespace 2, since then the Freespace Source Code Project has been upgrading the open source engine to make it compatible with modern computers, the graphics look nicer, ... and port it to Mac and Linux! In other words downloading the FSO engine makes the game a native Mac app. :)
Downloading is fairly easy - though potentially laborious if you want all the mods - the base engine is several Gigabytes to download and the mods add more on top of that. However, one of the mods is FSport which also lets you play Freespace 1 in the open source version of the FS2 engine - the only problem I had with it was a couple of the cutscenes not playing right, but I solved that by replacing the cutscene files that came with the FSport version with the cutscenes from the GOG version (different encodings) and they worked fine after that.
The link on the bottom of the site below for Automated Installer - makes installing the game straightforward: http://scp.indiegames.us/bnr_installer.php
Then also download Soulstorm's launcher (makes launching the base game and any mods you might want to play a breeze - even letting you easily tweak settings on the game should you so wish to): http://www.oramind.com/index.php/project-menu/mac-apps/fs2launcher-os-x
Apparently there is also a new cross-platform launcher, but I don't know what state it is in currently - it seems to be a public alpha build, so I would still use SoulStorm's game launcher: http://www.hard-light.net/forums/index.php?topic=67950.0
Here are some general instructions: http://www.hard-light.net/wiki/index.php/Installing_FreeSpace_2_Open
Right now the engine is on build 3.6.12 - but they should be releasing a new stable build of the engine, 3.6.14, soon* (* this is an open source project, so soon is a relative term! :P).
If you still want to play the vanilla version of the game in WINE, I can try to help you with that - the problem you're mentioning does sound similar to some of the problems other WINE games had with the mouse in certain WINE engines. But really you should play the FSO version - native mac app, new graphics, glitches and bugs removed - it's really, really nice. :)