For some reason, when I set a custom key for "crouch/sink," the setting is only persistent until the next time I start Nexuiz. Once that happens, the default settings of "shift" and "joy1" are added to my custom choice.

While the custom choice itself does work, I do not want the shift key to be bound to anything-- in other FPS, I use the shift key for "run," and so am used to holding it down out of habit in many situations. As a result, I keep involuntarily crouching in the middle of jumping or running...

Is there any workaround for this? As it stands, I just reset the keybinding to "c" only each time I start the game, but that's awfully annoying.

Configurations are only saved on proper exit via the menu button or 'quit' command, configuration files are saved in the .Nexuiz directory in Linux, or the ~/Nexuiz/data/ directory for Windows...

Find where your config.cfg is, and add "unbind SHIFT" to a file called autoexec.cfg in the same directory.