Welcome to the forum.
What version of QT Pro do you have installed?
I'm also not clear if you Imported into PrPro CS3, or into QT Pro.
Oh I'm sorry. I imported into Premiere CS3 from Quicktime. My computer doesn't have Quicktime Pro, just Quicktime. Any ideas?
Can you describe your workflow in detail. I am not sure what part QT plays in this?
What is the CODEC in the MOV files? This ARTICLE will give you some details on the .MOV "wrapper." Note: more references are made to the AVI "wrapper," but it's basically the same for MOV, WMV, MPEG, etc.
What version of QT Player do you have installed? The reason that I ask is because many users have had major issues with QT Player (Pro is just an unlock code) versions 7.6.x. The "last known good" version was 7.5.5. These later versions really mess up Adobe programs.