What version is being used? The latest is here. 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.
Did you stabilize any clips? Did you allow the project to fully cache, as verified by the completion of the green line above the thumbnails, and loading of the audio clips in the bin (top-left)? Be sure to Save Project AS, giving it a unique name or #, so as not to overwrite prior saves. Save Project (no AS) will overwrite. Then you're protected.
If the issue persists the best way to get to the bottom of it is to share. We'll take a look. It's easy, takes little time and can be private. Follow the PORTABLE project instructions here...
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.