I never had this problem before, but ever since installing CC on my Mac i've been getting countless Quicktime errors within both AE CC and CS6. In CC it crashes the program completely, in CS6 it gives me Error (4) reading frame from file... (86 :: 2)
I reboot the program and it sometimes fixes it, and sometimes doesnt, and even when it does work it seems to randomly work slow or it iwll work for a while and then start giving me errors a few minutes in.
I am on a MacPro with an AJA Kona with all updated drivers.
An other characteristic is that it will either fail at writing any quicktime files or it will encode them extremely slowly.
Moved from the Creative Cloud to the After Effects forum. They will be able to help you here.