Well I was having nothing but troubles with Nui, experience bar not working, chat functions not working and various other little things. Well after doing the "disable everything" routine I came to the conclusion my problems stemmed from using Carbonite. I switched from Carbonite to Quest helper and everything works, but now I have questhelper. I forgot how much I disliked this thing. Now I have to decide do I hate Questhelper more than I love Nui?
You should not be having issues with Carbonite and nUI -- A lot of nUI users also use Carbonite. There are some things you can do that help, but I'm unaware of any outright problems.
That said, the first thing that jumps to mind is the Carbonite Info Panel plugin for nUI. I'm not sure if it has been updated since I changed the nUI layout engine in 5.06.17 -- if not, and you have the nUI Carbonite info panel plugin installed, try disabling the plugin. You'll lose the carbonite map in the info panel, but it may solve your problem.
It might also help to disable Carbonite's built in minimap.
I'll leave it to other nUI/Carbonite users to chime in with any other suggestions they may have.
What people don't get is that I am, ultimately, an artist at heart. My brush has two colors, 1 and 0, and my canvas is made of silicon.