We had this problem with both our bunnies but especially Smudge. He had to have his incisors removed in December 2004 which didn't help him but it was also their diet. They were being given Excel Junior and Dwarf but we weaned them onto Science Selective and they now only get a handful between them in the afternoon. Treats are now limited and their diet is only a small variety of vegetables and a lot more hayinstead of loads of different kinds of stuff.
Blackberry leaves are a good way of getting their guts sorted out too.
Also, if your bag of Excel is still in date you can contact the manufacturer and give details required (see the back of the bag) and if you explain that it is making your bunny have runny poos you will get a refund for the price you paid for the bag of food. I seem to think we sent a copy of the receipt and a sample of the food too. Good luck.