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I don't use it myself but I do not believe any addon can specifically say it is incompatible with another one without mentioning it on its download page itself and not inside the game.
There are several other comments made on the curse website talking about incompatibility and none of them mention nUI itself.
So, basically, turn off all addons except for the EQCompare or EquipCompare and then see if it works. If not, then it is something to do with the addon and most likely nothing that can be done at nUI's end without knowing the error message itself.
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