Well nexuiz-sdl.exe uses libSDL to interface with the hardware while nexuiz.exe uses more windows-native methods to do so.
The docs to DarkPlaces (the engine) say:
Windows Input: -dinput enables DirectInput for mouse/joystick input
DirectInput is DirectX so you might want to try that startup parameter. Though i must confess i have little interest in looking closer at this stuff as i no longer use windows myself

And if it helps you feel better this negative mouse acceleration that can happen with non directx input is a windows xp bug which can be fixed by disabling acceleration completely for non direct x with registry changes. Back when still using i used that file:
http://esteel.planetnexuiz.de/misc/mous ... _off_1.reg