http://bugs.winehq.org/show_bug.cgi?id=58729
--- Comment #5 from ToastyBug cemer99797@isorax.com --- It seems the bugs when the game is running from the launcher app (JEDI.EXE) are caused by Wine's fullscreen implementation and the fact that the game's fullscreen resolution doesn't match the monitor's fullscreen resolution.
When switching away from (Cmd-Tab) and back to the gameplay, the bugs can be fixed by setting the gameplay resolution to match your monitor's resolution: 1. from the pause menu (Esc), select Setup > Display and choose your monitor's resolution 2. click OK and Esc Esc to back out back to the game
The gameplay resolution now matches the monitor's and will not cause issues, but the menus (pause and main menu) are still using the old resolution (640x480 or 800x600) and still have issues