Hi Mark,
just tried the exact same setup on a Mac Pro 4x3 Ghz and this problem did not occur. I only used the Eos Utility running in the background, every capture came into lightroom perfectly, the Quick Preview window doesn't pop up (i guess i switched it of once in the eos utility camera control window).
But hell it is slow compared to C1 and a phase back or a mk II.
I know this won't help you at all, but i think the conflict is somewhere else.
I will try it again on my MacBook Pro 2.0 and come back here.
cheers,
martin