Info log over lapping combat log.
 

Ok after many many bug worked out since the update.
I have been looking into using nUI again.
I notice that when i installed it the info log and combat log where out of place/not placed right.
I have reset everything and reinstalled just nUI and I am still having this problem.
I am running at 1920x1080

I cannot see your screen shot well enough to make out what the chat frame is that's on top of the combat log because you embedded it into the message. In the future, you can use the paperclip icon in the message editor (or scroll down the message editor page to the "Manage Attachments" button) to attach your full size screen shot to your message. It makes it much easier.

That said, have you tried unlocking that chat frame and dragging it onto either the combat log or the main chat frame so that it docs? Whatever that frame is, it is *not* a chat frame that nUI itself created.

Yes it seems to be an extra chat frame from somewhere but I am not sure what could be creating it. See what happens when you close it, log out to character screen and log back in again. If it goes away it is just an extra chat frame that an addon couldn't utilise.

My chat frame plugins should be named Chat, Guild, Whispers but I won't be surprised if 4.0 patches did something to change that so let me know if you have those and removing the chat frame like I mentioned doesn't relieve the situation.

I have removed all other add-ons and ran just nUI and it is still there.
The tab says "Info Log"

Info Log is a chat frame being created by something other than nUI... try right clicking the tab for the info log frame and closing it, then log out and back in and see if it comes back.

Thank you.
I was able to fix it.
upon first run it puts the combat box in a very weird place.
(It is nUI's box)
I could not right click it for some time, but I was finally able to and move it.

One thing to note in case people come across something similar. Chat Frames aren't actually removed. Blizzard sets up 10 frames for you ( whether unique per character I can't remember, one thing I need to check for my addons actually .. *makes a note somewhere* ) and stores it in the chat-cache.txt file in your wtf folder somewhere.

Even if you remove an addon that may have created it, unless it has a way of telling it to go away then it will always come back on login because blizzard simply reads through its chat-cache.txt file and generates and positions the windows as it has stored them since the last log out.

My addons do their best to minimize this problem by releasing the chat frame by either removing it totally or docking it to the regular chat frame. I know my initial tests had this working fine but we all know 4.0 messed some stuff up so maybe something there I haven't come across yet myself.