'Custom' is supposed to show up when you change config files. If it doesn't say 'Custom', then your config isn't working and you've put it in the wrong place and fell under a placebo effect. Fumbling about, clicking everything to get rid of 'custom' will screw your game up.
In other words: if it says custom you're doing it right! If the game's slow and screwed up, you're doing it wrong!
This goes for every config, not just xconfig - and they're all fragile so leave them alone in the game options or delete the actual config file from your root Crysis folder (or in the case of xconfig, use the uninstaller exe that came with it) if you no longer want to use it.