Hey Scott,
I'm having a couple issues with Nui.
I'm running Nui+ version 5. I have really basic addons running with it:
DBM
Recount
Omen
Bazooka
Auctionator
Atlasloot
vuhdo/nui window
Easymail
Crapaway
1) The tooltips for loot dropped (when you mouseover an item to see if you want to roll on it) flickers so you can't really see it. Not such a big deal, but annoying.
2) Today I was raiding in Firelands and everything was going fine with Nui until I hit this giant Bird Boss. (Alysrazor). These empty feather icons appeared over my buttons. Which wouldn't be a huge deal except it kept me from casting anything unless I opened up my spellbook.
So strange I know. I wish I took a screen shot.
I disabled nui and everything worked fine on our 2nd attempt. (I managed to wipe the raid on the first).
Anyway--I'm a level 85 Shadow priest. Dont' know if that helps or if you need any other info. I couldn't find any other bugs like this in the forums.