I had that problem on my first century for this year a couple of weeks ago. About mile 65 or 70, my butt started hurting and I started focusing on the pain. I stopped at a couple of rest stops and considered getting a ride in the sag.
But I was riding with a friend that is in his late 60 early 70s, and I'm at least a couple decades younger so figured I better do it. I also felt bad about making him finish the ride by himself.
The moral of the story is that we finished the ride. The pain actually subsided a bit at about 80 miles and I really enjoyed the rest of the ride. In fact, I felt really good when I finished, like I could have kept riding.
Sometimes, you just have to turn the brain off. You can be your own worst enemy.
Az