Does he stay clean during these episodes or is he covered in his own filth? Keeping fur clean is very important with rabbits who have messy poop, because rabbits with poop-smeared fur can get a horrible disease called flystrike
Please check his rear end and feet daily, and if your rabbit has trouble cleaning himself, please consult a vet ASAP.
Cecals are normal in small amounts, but if they’re fouling up the cage there’s something wrong with his digestion. The most common things that’ll upset his digestion are an unbalanced diet and/or the ingestion of fur. Many buns experience GI upset during their seasonal moults, and daily brushing helps a lot with that.
Diet is a bit trickier, but these are common triggers for messy poop:
– Not enough hay (experiment with different types to see which your bun likes best). Some rabbits don’t eat enough hay because they get a bit too much from their pellets already. Consult with the vet about their weight and right amount of pellets, and try to decrease pellet intake a little. This will encourage a rabbit to eat hay.
– “Rabbit muesli”-type food, these are made to look good for humans but doesn’t contain the right nutrients for a rabbit. Look for a uniform pellet with enough fibre and not too many sugars and starches. This is a website which compares brands: http://www.therabbithouse.com/diet/rabbit-food-comparison.asp
– Too much sugar or starch in other foods (fruits, carrots, treats, etc.). Rabbits evolved to digest low-calorie fibrous plants like grasses and herbs. Starches and sugars will upset their gut bacteria, this might begin with messy poop but may turn into potentially deadly stasis. Give treats only in small amounts, and as long as your rabbit is showing symptoms: rather don’t give these treats until they’re back to normal.
– Vegetables which trigger these symptoms. Some rabbits will get runny poop from eating too many vegetables or vegetables which contain too much water. (Our Breintje gets messy if he eats endives.) To find the culprit, feed hay and pellets only until your rabbit is back on track, then slowly re-introduce certain foods.
Hope this helps 