Hey Ronaldo–
I just went through exactly what you’re going through. QTPro worked for awhile, and then starting a couple months ago I’d get lots of flickering and weird artifacts at transitions. I spent three days poking around the web looking for free/cheapy converters, but nothing I could find worked worth a damn.
I finally ran out of time and sanity and caved and bought Sorenson Squeeze 7. It works great, but it’s hard to figure out and costs your first born child.