Is it possible she doesn't like the flap to the box? Twice now you have lifted the flap for her and she's gone in...Hopefully the presence of the lidless box will help. You may want to put box in the rooms she seems to really like peeing in.
It is also sounding more and more like it could still be a bladder infection, that's alot of pee for one little cat in an evening.
Here's a thought...does she drink more than normal? If yes, ask the vet to check her glucose...could be diabetic?