Calling '/nui rl' just executes the built in Bliz function to reload. I use the command probably 20 times a session since I'm constantly reloading to test code changes, etc. If you haven't done a clean install of nUI, I strongly recommend you follow the instructions in this FAQ:
http://www.wowinterface.com/forums/s...ad.php?t=21716
If you disable all mods except nUI and issue the command, does it still log you off? Are you getting any error messages? When you do a reload, how long on average does it take before you get logged off.