What is the format and resolution of those clips? What version of Videopad is being used?
With the sequence as complete as possible - including the frozen clips - please upload the project so someone can analyse it. This isn't difficult, takes but a few minutes 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 share it.