I got it figured out. I'll just go through each program, go into the .exe's properties, and change the compatibility settings to force them to scale correctly.
After running the upgrade to Windows 8.1 yesterday, I have ran into this one problem that I just can't solve... that being all non-Windows programs are being scaled up and pixelated... making for an unpleasant sight to the eye.
Here are some screenshots to some programs with this issue...