I’m having problems with Kega Fusion 3.64, only when being into Fullscreen mode. O.O I have a Notebook Samsung with Windows 8.1 as well, and Intel 4000 HD for Graphics alongside Realtek HD for sound, BOTH on-board. I have tested Fusion into Normal Mode (NOT Fullscreen) and it works just fine, even when loading one or another ROM. ;D
Anyway, I think Kega Fusion 3.64 DOES requires a major update, just because Steve Snake describes it to work only up to Windows 7 included only.
By the way, Tectonicman, have you tried updating the drivers for graphics and sounds; you know, it might fix several problems… =D