I honestly don't remember it exact problem now. It could have been firmness, or a lack thereof; maybe the shape, or even something else. I clearly remember the pain though....
If anything I found the stock seat was too soft, lack of support meant serious pain building up on rides of more than an hour or so. I got a Shad seat which is much firmer and in the long run more comfortable as a result. A side effect is that I now feel the engine vibes through the seat - nothing unpleasant but the stock seat was so soft it muffled them out completely