For about 7 years I was Tandem riding with very little Solo bike riding. The Tandem was set up properly for the Long offroad Enduros we used to do. Only problem I ever had was Butt pain after about 80 miles. That was one reason i used to prefer the metrics. But that Tandem was perfectly set up.

One Thing I noted though was that The Solo Mountain bike did cause a few leg pains- Not really cramps but the thighs would tighten up after about 3 hours riding and it was getoff the bike and have a good stretch. Then one day and like you I found saddle Position was different. Pedal to saddle was correct but the saddle on the solo was too far back. Put on an inline seat post to bring the saddle forward and Problem solved.