Ok. Her litter pan sounds to be about half the size it should be. I'm a little confused about what you mean by saying there is hay in the pan and in the pen. Do you mean there is hay over the floor of the pen?
The litter box should (aside from being larger) have litter in the bottom and then the litter should be topped with hay. With the right litter, it shouldn't need daily cleaning. In fact, cleaning it too often can sometimes encourage potty accidents because they like to 'go' where they can smell it. If the litter box is cleaned too often, then they may not be consistent in using it to potty.
If it is the case that there is only hay in both the litter box and on the pen floor (not sure if that what you meant) then that could certainly confuse a rabbit as to where she should potty.
With the right size litter box, however, the remaining space in the pen will now be rather small. It is easy to enlarge the size of the pen if you make use of one wall in your home. If the pen is shaped into a rough "U" then the space will be much larger. Here's a photo that shows what I mean:
The pen is also rather short. Most rabbits will easily hop over a 24" pen wall. If she hasn't yet, be careful that she may decide to at some point.
So in trying to get her more consistent, I would start with getting a larger litter box (I use sterilite storage containers as you can seen in the photo in the right corner). I would put litter (like wood pellets -- pellets, not shavings) in the box and top it with hay. I would also consider getting a taller pen, but also widen the space by making use of a wall or a corner (2 walls). I'd also be sure that there is no loose bedding or hay elsewhere on the floor of the pen.
