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nUI doesn't actually know that you're in a raid or not.... more to the point, it just shows or hides frames based on whether or not a given unit exists. It is otherwise blissfully unaware of what you're doing.
Now, that said, one thing that could be in play would be unit frame (aka raid) sorting which should not occur in combat. It's the only part of nUI I can think of that's triggered by the existence of a raid. However, if it did fire while in combat, it could be causing taint which would make your secure actions break and look like your key/mouse bindings/buttons were not working.
You can figure that out easily enough. While out of combat, change the '/nui raidsort' option to disable it (none) then do a '/nui rl' to reload. If the causes the mouse problem to go away, then it is the raid sort that's at issue. If not, then we need to look for something else.
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