I've had this problem for almost a year now. I saw my doctor in the spring and he suggested it was a prostate infection and gave me some pills.
The pills helped but didn't solve it completely. I went backpacking shortly after for a month. Possibly because of the excessive walking I noticed that for a few days puss was seeping out my anus. After walking for a few hours I would have to use toilet paper to wipe off what I assumed was puss (it was yellow).
That hasn't happened since, but for months it has always been uncomfortable to sit down. I would have to sometimes sit on one foot so my anus was not putting pressure on the actual chair. Whenever I make a bowel movement the first few seconds are slightly painful but when the other 80% of the stool comes out it isn't anymore. The more backed up I get the more uncomfortable it is. After I have passed a stool I find it less painful to sit down, so I try to stay as regular as possible.
The last time I saw my doctor he had no idea and just told me to send in a stool sample, blood sample, and spine x-rays. I never sent them in though.