Not necessarily. People aren't perfectly formed on both sides of their bodies, and often there is a discrepancy in the lengths of their legs, or in the angle of their pelvis.

A suggestion would be to go to a physiotherapist and have them check the length of your legs. It's a fairly simple process (the most accurate way is to have X-rays done). The PT then should be able to advise you on what you need to do to compensate.

In my experience, seat height does become a critical factor on long distance rides, because the continuous pedalling will find out something that won't become evident on shorter rides. You may be at a point, too, where a mere millimetre of 1/32nd of an inch will make the difference between pain and non-pain.

You do need to rest and ice the sore spot though.