I had a problem with the fresh install and it had to do with the convert commands in the video_conversions.php.

I had to use the one from 2.4 or 2.5 (I can't remember now sorry), it was something in the newer version of the convert commands in there that the ffmpeg thingie didn''t like, so I went back to one that I knew worked and haven't had a problem.

It's the include/settings/video_conversions.php

I'm suspecting you might have same issue. If you want, I can send you my video_conversions.php file for you to test out.