Oh, and Oldpcuser, that brings up fond, old, childhood memories. Back on that Windows ME machine with a CRT, it used to boot me out of the game all the time! I simply learned to click the minimized Battle for Naboo window in the Start Bar so fast that it didn't affect my game play! Next time it boots you out, look at your Start Bar. Is it minimized in there? Just click it, and you should be back in the game. I hope your situation is solved this easy. You might not be having the same exact problem I had. I hope for the best. Have you tried WINE + Linux + CDEmu + BFN yet?
And Pedro the Hut, you're probably thinking of compatibility mode. I tried that for Battle for Naboo, and it didn't help the the computer that was having issues with BFN. Read my story
! But WINE + Linux + BFN + CDEmu DID fix it.
This game is a part of my childhood and growth to geekdom. I have returned with the answer!