Perhaps the cache is corrupt. OPTIONS | DISK tab, Clear Unused Cache Files.
Do this after restarting Videopad, and prior to loading the saved project.
Of course, Save Project File AS routinely, giving it a unique # or name, so as not to overwrite prior saves. Using Save Project Files (no AS) will overwrite. From the HOME tab, that choice is available by clicking the caret to the right of the Save Project button on the toolbar.