Could be the cover for several reasons
- she doesn't like the smells it captures
- she is too big to sit comfortably with the roof over her head
- she feels claustraphobic with the enclosure
- she is arthritic (I don't know her age) and the cover makes it too awkward for her
- some other eason (She hasn't actually spoke to me! )

Try taking the cover off. My Mr. Amber Cat refused to use boxes with lids, never did figure out why.