Tonight the nQuake package has been updated with a couple of changes:
Set the default ruleset to "Thunderdome" as that's the main tournament around these days.
Fixed a configuration issue that lead to the nQuake HUD and rest of the configuration not getting executed on Linux under certain circumstances due to conflicting autoexec.cfg files. The nQuake HUD shall look like this sample screenshot and nothing else also on Linux now. (thanks to iBurley for reporting this)