Right. FFMPEG works just as well on windows. That part is ok really.
The biggest problem is usually that people download all the mods they want, but not the filter. Then Moodle complains because of the dependency on the filter. So they try to download the filter, but it is 18MB, and so sometimes the connection to Moodle.org times out. Then they are stuck.
The thing to do in this situation is to upload the filter via FTP , or download and drag 'n drop it into the plugins installer if the file upload limit is greater than 18 MB.
Anyway the point is that in some combination of the above, the site probably got in a state. It would be best to re install the filter and get it working properly. And probably re install the OnlinePoodLL assignment submission plugin too.
Sorry for the hassle. Incidentally I am working on a PoodLL app to make ipads and friends work better.