Bad bike fit can certainly cause painful problems. A perfect bike fit isn't a guarantee you won't have pain problems. For most folks, centuries are at least a little challenging, at least a little longer and a little harder than our normal rides - so you learn to ride in a way that keeps the pain tolerable. If you want to call that discomfort instead of tolerable pain it's OK with me. When I finish a century feeling good... I'm still hurting a little bit. And a new rider ought to expect that pain management is going to be an issue.