Have you tried a different loader (like Neogamma)?
I'm pretty sure you're launching backups from DVDs - have you tried USB Loading?
Some of these issues can be solved by doing these things.
Also check that you have the latest cIOSs (I use d2x).
EDIT: Btw, I hope you know that the game will not run without motionplus, right? After all, you DO own the game.