Yep. That was it.
It was a long shot but glad it fixed it.
Apparently the folder with the ffmpeg.exe doesn't get wiped when uninstalling and reinstalling the software.
So I removed the entire \users\username\Appdata\Roaming\jAlbum\bin -folder, uninstalled Jalbum and reinstalled it.
And now it works. Thank you both for your help.
If you get the same problem again try deleting just the bin folder and ffmpeg file, jAlbum will create a new folder and file as soon as you try to process a video.