That exactly what I thought before I flipped the stem! In theory, if i understand it correctly, the saddle height has to be set by the legs length. And they do not change (I hope). However, I had to raise my saddle several times after being fitted, (before flipping the stem) the same what OP did. but in my case I got uncomfortable after stem flipping. the same as OP who has hamstring pain.
Does it mean that he and I had saddle height wrong and stem flipping helped us to discover it?