Sure, I'll give it a try.
For example, if I fire up Super Mario Bros on FCEUltra, when I press 'right' on the joystick, it takes a second or two for Mario to move right. Same with every other direction, jumping, etc. The same keypresses provide instantaneous freedback in windows and even MAME, however. I'm using an IPAC4 in USB mode if that matters. This all started happening right after I upgraded windows.

I would have assumed it was just FCEUltra, but I get the same exact behavior in ZSNES.
Let me know any other information which would be helpful.