Litter box training problems

Question
Thanks for the quick reply.  I've been using wood shavings in the cage.  The vet actually suggested taking the shavings out.  She felt that maybe the bunny feels with the shavings, the entire cage was a litter box.  She suggested just putting towels in there and that would encourage her to use the box.  I tried that and it was a big mess.  I'm back to using shavings.
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-----Question-----
We adopted a 3 year old rabbit a few months ago from a friend.  The cage the rabbit was housed in was way too small.  About 2 ft with was litter box and she was never litter box trained or spayed.  The first thing I did was but her in a much bigger cage and put in a litter box and filled it was hay.  We use the old cage as her litter box for outside the cage.  She can get in and out of her cage on her own and has an entire room to herself.  We also had her spayed about 2 months ago.  Inside her cage she uses the entire cage as a litter box.  I've tried different things and she just goes wherever including urinating in her food dish.  Outside the cage she is much better.  She uses her litter box most of the time but lately she found a few spots in the den (we let her out of her room when we're home) that she likes to leave droppings on and then nibbles on them.  She never urinates outside the litter box when not in the cage and I realizes nibbling on the droppings is normal behavior.  I've tried different things to get her to go in the box.  I'll put the droppings in the box and then put her in.  I don't know if the problem is something I am doing wrong, if it's her upbringing, or I just happen to have the Oscar Madison of rabbits.  She does groom herself often but doesn't seem to care about keeping her cage clean.
-----Answer-----
Hi jeff,
you're not doing anything wrong,thats for sure...quite the contrary! She's lucky to have found you as her new friend...
 Did you try using woodshavings inside the cage litterbox? This could help....and it's easy to clean.  When they urinate on the straw it gets wet and stays wet...making it uncomfortable for her to use again...whereas woodshavings dry and absorb odor and wettness...making it more attractive for her to go into again,,,this may work.
 Try and let me know, and always use pine shavings cause cedar is toxic for them..
all the best,Elizabeth

Answer
Yes,it would make quite a big mess! But only put the shavings in the litter box...and nothing in the rest of the cage.  It works very well for me.  the floor of the cage doesn't bother them especially if they are allowed out once a day to romp around.
 Good luck,Elizabeth