Have you ever right-clicked on the specific game entries and disabled the game-specific hacks? (highlighted below)
I don't understand why Paper Mario and Twilight Princess hacks are on by default. They should be unchecked.
No I hadn't done that. I unchecked those however and I still get the same issues. Being in IT I would tend to think the issue is with my system but all other games play great and PCSX2 runs great. I just don't get it. Any other idea?