I had this same problem and nearly went mad, as more and more glitches like the ones you describe kept popping up in my projects as I worked on them. It’s definitely related to the compression codec that Flip Video uses. I updated the software via their site today (9/29/09), and this update installs an updated version of the codec which, oh so mercifully, seems to have completely solved the glitch problem for me.
link to software update:
https://www.theflip.com/app/prius/31/update/index.aspx
Best of luck to you,
Scott