My first thought is your rabbit has coccidiosis, possibly hepatic coccidiosis. It can cause poop abnormalities like that, the hepatic one affects the liver which could result in issues with bile production and green poops as a result. Hepatic coccidiosis can also result in ill thrift, weight loss, wasting along the back and hindquarters, rough coat, etc. Your vet could see if it will show up on a fecal float test, but sometimes the test may be inaccurate, especially if it's the hepatic kind instead of intestinal. So it may be advisable to go ahead and treat based on symptoms exhibited, with a sulfa antibiotic or ponazuril/toltrazuril.
http://www.medirabbit.com/EN/GI_diseases/Protozoal_diseases/Cocc_en.htm. (contains graphic medical related photos )
The other possibility that comes to mind is a liver issue other than coccidiosis, in which case a blood test and possibly xrays, may be needed to help determine whats going on