I do remember this when I was testing things out initially. My board's two x16 slots skipped a GPU spot so it was lower on the motherboard, but when it was x16x8, next to each other and the lower one was higher, the bottom one required careful cooler placement.
I did have one instance in the x16x8 setup of a 10+ degree difference under load though, and that was corrected by taking the RAD out out while the card was under load and elevating it above the card while shaking/tapping it slightly. This, I believe worked the a water bubble out that had been caught where it wasn't supposed to be (presumably in the block). I then carefully lowered the RAD back to its spot paying special attention to keep it perfectly upright (with the top of the RAD, but not the whole RAD, still above the GPU plane).....and it dipped back down.
You can give that a try, but honestly a couple of degrees is no real issue with as cool as they run anyway. It could also just come down case airflow, with heat being pocketed in between the cards.....or a different thermal paste application from the factory on your second card.
Just out of curiosity, have you tried flipping cards to see if the heat issue follow the card, or is it all about position?