I have 7 litter trained house buns. They do go in there litter boxes about 75% of the time. The other 25% may not seem like alot but multiply it times 7 rabbits and it accumulates. They have been in the same environment for over a year and I have tried several methods. 

I have tried:

• different litter materiel
• putting fresh hay in frequently
• putting water bottles above litter boxes so they have to go in box to drink
• putting all poos (they only poo outside, not pee) inside box
• rewarding for going in box
• adding multiple boxes (have 5 now)
• re-litter training (never improves habits)

Their environment is my large enclosed patio. It is a neutral temperature probably between 65 – 82 F year round. They have lived in this 400 SQ FT space for over a year now and honestly love it. They have in the middle of my patio a large exercise pen with a door. I leave the door open because I have the main litter box they go in about 50% of the time. This is also where I put them when I re litter trained them. The other litter boxes are on the patio outside of the pen and they use these occasionally. They are all spayed/neutered and bonded. They love each other and are pretty laid back, loving bunnies. Hay is placed in the litter box frequently and I clean it about once every other day. Their pellet/treat bowl is near the main litter box in the pen as well. I cannot think of any other reason as to why this is happening. 

Before this they roamed my apartment and were fine, never had that problem. But it has been almost 2 years since we lived there so there environment is not new to to them.

Here is a URL of a photo of their environment (it was too large to upload) This is just after I cleaned it as well!

To view the photo larger: http://s32.postimg.org/la0rnh1bp/20160327_123245.jpg