I'm curious to know why this issue even happens. Why are the mouse drivers for the touchpad being coded to scroll only for certain somewhat hardcoded application entries? Why not just have the driver say "I'm a scroll wheel"?

I've had no issues using the two fingered scrolling in Windows on my Macbook in any app, so clearly there is a proper way to do this.

Oh well, guess this is yet another odd mystery to chalk up on the Windows side.