You are drifting away from the topic
I found out something about Banjo Tooie:
I think those pauses and crashes are the same. I mean, when the game pauses it seems like the cpu just has too much to do, even if i don't know yet if it is cause by the video plugin or not. Sometimes when it pauses, it just freezes.
To solve this: If BT freezes hit F2 to pause the emulation - wait some seconds - press F2 again and voila, the emulation goes on and you can advance in the game
Please test if it works for you too.
Should be mentioned in the rominfo/next game database, shouldn't it?