Thanks! I was using FCP to convert and see the error of my ways. I used MPEG Streamclip to make an uncompressed file and the red flashing is gone.
The older computer is a first-generation Intel macbook pro, and it’s in a custom Flash player in Firefox. It’s been reported that there are still problems with the new video, but it definitely seems more stable from here.
In your experience, is uncompressed the best option? Should I be trying something else? I’m actually changing the frame rate to 30 rather than 29.97 since we ultimately want it at that rate for multi-media navigation purposes. Does that have an effect?
I’m a little out of my league at this point and really appreciate the help.