I've run into issue while testing mm_ffmpeg (2.x series) with ffmpeg_wrapper (2.x series) -- basically the form being leveraged by mm_ffmpeg via ffmpeg_wrapper_ui_configuration_form() has it's settings organized into sections i.e. $form['ffmpeg_wrapper']['audio'], $form['ffmpeg_wrapper']['video'], etc. But when the params are referenced by functions like ffmpeg_wrapper_convert_file, they do not include the sections -- so end up empty when executed. Also, where the default_values are set, they also don't reference the sections so saving the form doesn't save many of the values.

I have two patches which resolve this on our development site by changing items like:
$params['ffmpeg_video_custom'] to $params['custom']['ffmpeg_video_custom'] in ffmpeg_wrapper.module (in ffmpeg_wrapper_convert_file), and then another patch for ffmpeg_wrapper_ui.module that makes the same changes where #default_values are set on the form...

Mostly I'm just wondering if I'm missing something obvious before I post those patches... or if there was a recent change that caused this.