Sorry ekr, I wasn't replying to you. I was replying to Mindfreakbabe's original post.
I don't know what the issue is with your files. Flip makes iMovie compatible files, so if they no longer play correctly, then you likely have another issue with your system and converting the files won't help.
Have you tried opening Disk Utility and then do a "Repair Permissions" on your start up drive?
Patrick