If you do a '/framestack' over those greed spaces in the button bag, what turns up?
I'm wondering if the button bag code is picking up some frames off of the minimap and moving them/displaying them even though they should be disabled.
Xrystal -- have a look at the framestack. Also, look at the [WTF > Accounts > {account name} > Saved Variables > nUI.lua] saved vars file to see what stuff nUI moved into the button bag... that might give a clue.
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