I hear that....after I had my fitting in July, all my aches and pains went away. I just had another fitting recently by someone else to resolve a cleat issue I was having, and he moved my seat basically back to my old position, and wanted to further lower my seat and move it forward by another centimeter (said my problems weren't cleat related). That position lasted 2 days....all my old pains came back immediately, so I moved it back and was immediately comfortable again. Proper bike fit makes all the difference.

Standover height doesn't mean much, BTW.