I think this happens when the Library Part that is referenced by the Favorite cannot be found in the loaded libraries.
I don't know whether Favorites identify library parts by name or by GUID but I would suppose it is GUID.
I suppose when you double click the Favorite it applies the Favorite settings to become default settings of the Tool. At that point it will realize that there is such a Library part in the library, although with a different GUID. So the Favorite turns enabled. I think at this point you should resave that Favorite, overwriting the previously greyed one.
Please note that this is a theory on my part, I don't know if this is really the case, I have not digged into it that much.
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