if it is just the hands, it may be a bar height/stem length issue coming to the surface. since every one's physical compostion is unique, so will the body's reactions to a bike set-up. personally, I have never had the same break-in time/settling-in experience as anyone else. Similar? Yes, but not identical.
It may also be all the squishiness of the grips pinching nerves in your hands. I have had similar experiences when I stopped wearing padding cycling gloves/changed bat tape thinkness.
Try a few small variations on your current set-up and see what the effect is on the problem you are experiencing. no one can truly and fully dial-in a bike but the owner. and learning a little bit how to do it yourself will help you to get it where you want it. make sense?
and welcome to the FG/SS forums...