Yes. While running Banjo-Tooie do:
Step 1) In Project64 go to the Options menu and select
"Configure graphics plugin..."
Step 2) Now assuming you have unchecked "hide advanced settings" if not do that now and press ok and repeat step one... If you can see "rom settings" tab now then go to step 3
Step 3)
Click on the Rom Settings tab and uncheck self rendering textures then click ok, problem solved... but you won't get a movie picture!
Only do this before and after that part as other parts of the game need this effect and don't cause any performance decrease
Recheck "self rendering textures" when you're finished with the moving puzzle.
hope that helps...