After the MacBook Pro Retina EFI Update 1.0 update released by Apple for MacBooks Pro Retina, some users including this one who wrote to you started to find performance losses during the use of the machines in times of intensive graphics use, when the machine returns from rest or when running Windows via Boot Camp.
According to what was reported in several topics on Apple's support forums, the problems are caused by a underclock both the GPU and the CPU of the Macs, when temperatures considered to be very low are reached, causing problems with frames. According to the website AppleInsider, the MacBooks Pro Retina processors should start their temperature maintenance actions when they reach 105C but, after that update, this has been occurring at 80C.
Some users have found some improvement on Macs after resetting SMC and / or PRAM, however, the solutions are temporary and only last until the next lap of machine rest. If the performance issue was actually caused by this update, a new version of the EFI update should address the issue; it is now up to the users to wait for a definitive solution from Ma.