Hey George,
VideoPad 3.00+ stores its cache files in "C:\Users\<yourUserName>\AppData\Local\Temp\VideoPadCache". For example, mine is in "C:\Users\Connor\AppData\Local\Temp\VideoPadCache". You can delete this folder safely while VideoPad isn't running.
Alternatively, you can close VideoPad, re-open it, open the "Options" dialog and click "Clear Unused Cache Files" on the "General" tab, which does pretty much the same thing as above.
Also, this problem may be related to the one outline here: http://nch.invisionzone.com/index.php?/topic/19803-loading-times-241-versus-304-and-cache-file-contents/
How exactly were you using the program? Making a lot of cuts in the clip? Did you reload the project many times? Thanks.