It is an issue with windows/mac compatibility. So I need to either find a way to remove the extra file or create a PC compatible file.
Interestingly, there is an export function on the Lion version of QT that allows you to export a PC compatible file. This WORKED! Caveat is that it will not convert a file that has been output directly with Apple Pro Res 422 from FCP. So you need to compress the file elsewhere (using Compressor or third party app) then bring it back into QT and then export as 1080 compatible with Mac and PC. I would like to not have to compress the files as much, but it still looks great.
This was a total hassle and it was nice to find a solution. Still find it strange that I have to process the file twice to get it to work. So any other/better solutions are welcome!
– Jet