I've now found that even when using the MBII client I have similar issues while holding the crouch button. When I use Moviebattles II through the MBII client (which uses openJK) the issue seems to go away there, however, it still persists in single player, and prevents proper Steam Integration. I have tried using openJK but that didn't fix it. I tried installing Jedi Outcast as well and I can't walk straight forward there either. I removed the mod and completely deleted every single file relevant to the game and then re-installed and it still won't work, a process I've repeated several times. I then found that I had a similar issue in the base game: in single player walking straight forward would cause my character to slow down and play a weird bouncing animation, however, multiplayer worked fine.
While playing Jedi Academy with the Moviebattles II mod on Steam I suddenly had an issue where if I tried to walk straight forward my character would freeze.