I had a similar problem with one particular bike I couldn't get comfortable on. It turned out that because of an odd geometry the centerline of my saddle was too close to the centerline of the bottom bracket compared to my other bikes. That changed my pedal stroke which affected my back. A couple of miles into a ride I would already be sitting up and stretching it. So I slid the saddle back 2cm, installed a shorter stem and it was good to go. Even if your fitter adjusted your saddle so your knee is over your pedal spindle that doesn't mean it's perfect for you since no body is the same.