Since you have three boxes, I guess that leaves the location and the litter. Make sure you use an enzyme cleaner to clean up any messes, even if you smell nothing. Do you have a lid on the boxes? That makes the odor much worse when the cat enters. I use the Littermaid, which keeps the litter cleaned. That might also be helpful. Good luck.
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A dog, I have always said, is prose; a cat is a poem. ~Jean Burden