I am trying to bind Mouse4 to the CryLink and Mouse5 to the Nex. I couldn't do it ingame; the buttons didn't work. So I did it manually in the CFG file, and now in the settings it shows up as bound to mouse 4 and 5, but the actual buttons still don't work. I am using a razer diamondback with the latest drivers and mouse buttons 4 and 5 work fine in every other game. Can somebody please help me? If it means anything I use nexuiz-sdl.exe.

As far as i understand it this is a problem of windows and libSDL which does not support all mouse buttons. nexuiz.exe should be able to use more mouse buttons. But i'm not sure if it can use all mouse 5 buttons.
Also every other game? I remember quake3 had similar problems when i was still on windows. The solution i used is to put keys on buttons 4/5 in the razer driver that way those worked in every game. An other game i know that is not able to use buttons 4/5 is cube/sauerbraten.

whats the difference with nexuiz-sdl and nexuix.exe? I want to make sure I am using DirectInput. I just tried nnexuiz.exe and it works, but does it use DirectInput?

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