Sorry to hear about your bunny.
It could be a mix of problems that causes this.
Rabbits generally eat a soft gooey poo that comes from their anus, this enables them to gain more nutrients from the grass/food that they are eating.
If they have become over weight sometimes they are unable to reach and thus everything becomes stuck around their anus. If he is an older rabbit this could be part of the problem too as they become less 'flexible' as we all do when we get older!
Another thing would be to have his teeth checked as their molar teeth can become long and over grown which would prvent him from grooming and cleaning him self ad he should be.
Make sure that his diet has plenty of good quality hay available all the time as this helps to keep their teeth and intenstines in good shape.
It is good that you are cleaning the rabbit daily as it is all too easy for them to end up with 'fly strike' where flies lay their eggs on the poo and the maggot hatch causing infection and pain. They can so quickly get sore in this wituation.
I hope he is better soon.
regards
Selena