If you have general problems I wouldn't concern a fault with SH3 or some mods here at first.
Because you just upgraded your hardware I assume you did a complete reinstall of Windows on a formatted HDD.
Perhaps there are some remaining driver issues ? Reinstall DirectX.
You could also try not using the very newest graphic drivers as one version older ones do run more stable sometimes. The same for the mainboard drivers.
One thing I experienced when switching to a TFT screen was a noticable lag in performance in some games when relying to the standard windows drivers for it. Installing the special ones for the screen did it there.
I also heard about using the DVI connector instead of the VGA can result in similiar problems from time to time.
No special advices there, sry. Never had this but it sounds like something hardware/driver related to me.
Hope you fix this soon, i.
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