On Windows, i had several Nexuiz versions and it was fine, but on Linux every version creates the same ~/.nexuiz folder with the config, so it all uses the same config. Am i confusing something or what can i do?

That is the default behaviour on linux.
Instead of explaing more I link to Greens tutorial about multi-user commandlines http://www.youtube.com/watch?v=B4CEMkQ4x8o

Oh, i know Linux does this by default for all applications. My choice of words was just inconvenient. Thanks for reminding me of GreEn`mArine's excellent Nexuiz In-depth podcast, i haven't had time to watch all videos, yet.