Worth getting her checked at the vets' if you haven't asked them about it, she could maybe have a urinary tract infection. Sometimes cats can associate the pain on weeing with being in a tray and it puts them off going in one. Other thing is is she neutered? An un neutered cat will pee around the place.
How does she get on with the other cat? If she is shy she might not feel comfortable sharing a tray, and perhaps another tray would help?

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