I've tried standard HD resolution images (designed to match my sequence), as well as some stills smaller and larger than the standard HD frame.
I can throw whatever image size I want at the timeline in Mercury Software Mode and there is no effect on system speed (except losing the speed increases from GPU mode).
I'm just frustrated that I seem to not be able to use the benefits of GPU mode if I incorporate a still into the timeline.
Also many of the images I'm working with have been used in CS 5.5 projects (of course there is no GPU acceleration for Macbook Pro's in 5.5)
So I quickly put together a generic PC with a i7 3770 CPU, 16GB RAM, and a GTX 560 ti (and used the Hardware GPU hack) and dropped the same project I have been having problems with on my Macbook Pro and lo and behold it works prefectly in software or GPU mode. I guess my issue is Mac related (OS/conflict/whatever).
Have you read in the "mac serious error" thread for other CS6 ideas?