recent bad litterbox habits

Hi everyone!

So I have a 6 year old lop rabbit, and recently her litterbox habits have been terrible. Very recently (this past week) she has stopped jumping to the upper levels of her 3 story NIC cage. The second level contains her litterbox and hay, and the third her pellets. She knows that that is where her food is, she even has reached up looking at the hay, but she won't jump up there. I thought at first that maybe it was because I moved back home from college so I had all of these backs in my room, and maybe that was upsetting her, but she didn't seem upset at all. She was still lounging around my room and wanting attention and hopping through all my stuff.
Well, now all the stuff is gone, and I've built her an additional little shelf to use as a step to the second level of her cage. Last night I put her pellets on that shelf, but she just reached up there and dragged the bowl towards her to avoid jumping up there. Luckily, with the persuasion of craisins, I got her on that step, and it took a while longer for her to get on the second level. She still hasn't gone to the third level of her cage, which still doesn't have a step. But this whole not jumping up to the second level thing has caused her to use her litterbox less frequently, so there is poop all over her cage. In addition to this, this past year she has gotten in the habit of eating her hay while her butt is outside of her litterbox, resulting in a very very messy cage.

Sorry for the long post, but if anyone can help me, I'd appreciate it.

Is this the same cage she's always been in? Has anything in the cage changed? What is the flooring? Some bunnies need traction or they won't jump.
I'd also say a vet check is in order because it sounds as though jumping might be painful for her and that might be keeping her from going to the upper levels. For now I'd put her food, water, and litter box all on her lower level if it will fit.

Yes, this is the same cage she's always been in. :/ It may be the traction thing. I used to have some carpet on her second level, but since she kept peeing outside of her litterbox I had to get rid of it. Maybe I'll put a new piece there and she how she responds to it. Any ideas on how to get her to sit fully in her litterbox while she eats hay and goes to the bathroom?