How are you measuring the temperatures, and where? The engine only has one engine temperature sensor, and it's in the front cylinder head. If you are using some kind of contact or noncontact thermometer on an exterior surface, I'd suggest your test method is probably responsible for at least some of the difference.
Is the bike completely stock, or has it been tuned? Is the EITMS enabled (rear cylinder shutdown)? It's unlikely the stock tune would be running the rear cylinder so much richer than the front that it would cause this sort of temp difference. The stock tune has to comply with emissions standards, and the amount of excess fuel required to cool the rear cylinder that much would be ridiculous and illegal. If someone has done a custom tune then anything is possible, but that much difference just due to excess fuel in the rear cylinder is hard to believe as well.
Jerry