How to import many .MOV files to Sony Vegas?
This is a known problem. Quicktime for Windows is 32-bit only, and that presents a memory ceiling for the QT handler/decoder. What's worked for me, including in a current project, where I'm working with hundreds of of 5D MkIII files, is to import in batches. Once done, I have no issues loading or working with the project even if many of those are used on the timeline. I should say that often I'm able to import many clips without needing to divide the import step into batches.

As suggested in the linked forum thread, try rolling back to QT 7.6.2 or Quicktime Alternative, and see if that provides a more permanent solution.