I'm sure there is some difference due to your sitting more upright, your knees maybe being at a different position over the crank, different seatpost offset, saddle height (as you mentioned), different gearing and bike weight... well, yeah, lots of factors, but nought that you can't dial in and get used to

I recommend a deep hot bath tub, candlelight in the bathroom, some pink floyd and a glass of cold white wine... let that pain wash away!