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Deleting the nUI folder is not, in and of itself, a clean install. A clean install is deleting *all* addons and their saved variables (more or less) if you follow the directions in the FAQ.
The idea behind this type of a clean install is to eliminate as many "unknowns" and "artifacts" as possible to get a "new" UI. If you follow the directions you start out with nothing except nUI and a brand new set of saved variables at which point, if you still have a problem, then we know something we didn't know before. If you don't have a problem then you can start adding your other addons one at a time looking for the problem to appear... if it reappears, we know where the conflict is. If it doesn't then the problem was an artifact of old addons which isn't uncommon.
In any event, the benefit of a thorough clean install is that no matter what the outcome, we have a "known" set of conditions which makes debugging the problem much easier.
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