Count me in as another person with this problem. Just bought the 2.7/16/512 yesterday, and upon loading my usb3 drive for a 50gb transfer, the fan goes to full less than 30 seconds in. I have the machine sitting next to both a 13 and 15 2012 rmbp, and neither one even has a fan goes crazy on handbrake. I was so impressed with the two refurbs I bought, I said "what the ****" and bought a brand new high-end model. Turns out, it doesnt feel so high end.
WIll be going to apple today, showing them the issue, testing it with a machine on the floor, and leaving with my money if they all do it. Not for 2700$. Ever.
EDIT: oddly handbrake does NOT max the fans out (cpu states 100c), so this appears to be an issue on my box with USB transfers (cpu states 40c).