What version is being used? Here's the latest. For licensed users upgrades are free for up to six months from purchase date. After that, VP will continue to fully function but a fee will be required in order to register the newest. Retain your old install file and registration info.
What is the resolution of the bulk of the clips and how long is the project?
The best way to track this down is to see it just as you do. Not the export, but the PORTABLE project. Please share it as instructed in the link. It's easy, quick and can be private.
Here's how... http://nch.invisionzone.com/topic/23659-tips-for-getting-help-on-this-forum/
If it contains sensitive material link it in a personal message (PM). Click the envelope above. It won't be passed on or retained. Use FILE|SAVE PORTABLE PROJECT AS, not simply SAVE PROJECT, and don't forget to get a shareable link to post.