Def get a bike fitter's opinion, but it might just be that you haven't "trained" your body to accept the rigors of cycling yet. My gut feel (non expert!) is that it's more the former and less the latter. Get your fit tuned-up by an expert and keep putting in the important base training miles while making sure to alternate your riding position (drops, hoods, bars, standing, sitting, etc) to acclimate your body (and butt!) so you can nail those centuries coming up.