I've been having a minor bug or issue. Every now and then, the jump function gets unbound from the spacebar, and I have to reset it manually in the options screen.
Anyone else having this problem?

Very strange issue.
You could try going to the Arx install diectory and making cfg_default.ini read only.
Just right click the file, go to properties and check "read only", then ok.
That should stop the game from saving any settings so it could stop it from changing your key bindings. Also, you'll have to uncheck read only if you do actually want to save any of your own settings in the future.