Hey!
I'm not an expert or anything, but if you check under Options, go to settings (make sure you don't have 'hide advanced options checked'), go to the 'Advanced' tab, there's a bunch of stuff you can do there. Make sure anytime you have an option of Recompiler or Interpreter, you choose recompiler. 'Self - Mod Code Method' I think should be set to 'Check Memory Advanced'. Advanced Link Blocking doesn't seem to cause any problems, if Paper Mario can't handle the expansion pack, then make sure the memory is set to 4MB. Now go to the tab next to it called 'Rom Settings' (you can only affect this one if you have a rom playing. You'll see most of the same options. Play around with the 'Counter Factor' settings, that was what gave me problems with Goldeneye. It made my game glitchy and jagged when I set it too high, and it wasn't good low either, so play with it. If it's not any of those, you might want to check all of your graphics pluggin settings (including the advanced ones). It might even be the sound pluggin for all you know, if you're using Jabo's, then 'Sync Game to Audio' usually helps, sometimes doesn't. If you really like the game then you'll take time to figure this out before you keep playing it,
Again, I don't know anything, take care mang