I didn't think about Handbrake. I just converted a short clip from my phone (Mov. format) to MP4 H.264. I could have done that for each clip I'd used in that video, and then I wouldn't have to worry about the issues caused by Quicktime files.
I looked back at one of my clips for Half-Priice Books, where I'd filmed the software section of the store. I had a clip before it that was filmed in 720p using a digital camera and the rest was Mov. files. The section filmed with the camera still looks good, while the phone sections turned to ass.
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