It's not the switching that caused it. It's because the screen uses a custom color profile.
Certain games/apps disregard the color profile or ask a for a different one so the original yellow-y profile gets thrown out, and you end up seeing the native colors of the screen, which is blue.
BootCamp manages its own color profile, so you'll see the screen blue all the time... unless you calibrate it.
There is no fix for this under OSX that I know of. Not even if you were to swap for another MacBook because that's just how the display is. The rMBP doesn't suffer from this, by the way, since it uses a different screen technology altogether.
I have the same issue with my MBP2010 since upgrading to mountain lion. It's definitively a mountain lion bug (resp. driver issue) which messes up the color calibration while switching to the external graphics card. With Snow Leopard or Lion running on the same machine I never observed this strange behavior. You can "fix" this problem by logging off and in again but the issue will pop up again when restarting the system. I hope Apple fixes this issue soon.
I was able to fix this by resetting the PRAM. While the Color profile is correct, as switching profiles selects different ones (it is a good idea to run Color Sync Profile repair), I was only able to fix this by resetting the PRAM (hold down CMD-OPT-P-R while turning on from shutdown and let it restart twice)