Monster Hunter Portable 3rd HD VER

[TheDax]

There could be multiple factors: New settings introduced that are on by default which this game doesn't like, the same default settings aren't being used to test both emulator versions, winrot/the PC could've changed a bit since then, debug logging spam could be running on one, but not the other, emulation accuracy improvements could've slowed things down a bit, etc. It could be one or all of the above. Hard to say the exact cause without any more details.

Try turning off debug logging, and software skinning, if you have it on. Those are the two biggest performance droppers for this game.