I had problems with my backside all through this spring season until I had a week off cycling. I think I started too hard, too long rides too often, and I ended up with a sort of permanent bruising on my sit bones that never quite got the time to heal.
After the break I've been fine, I do get a bit sore on longer rides, but nothing really serious. I always tend to ride standing a bit more towards the end of rides, though...