Don't know if you still have this problem, but I had similar issues when I switched from Win XP to Win Vista. And I'm gonna tell you smth about Tunebite, so don't go angry

On XP Tunebite worked perfectly, but on Vista it was completly blind on the video aspect.
After a few emails back and forth with the support team, I found that if I disabled the hardware acceleration on my video card, I could convert w/o problems. You could try this, maybe it helps
I am using an Intel on-board graphic card.