No longer playing video on iPad after update

Hi,

So updated to the latest iPad Plex app this morning and had to manually update the Plex server running on my Personal Cloud to version 0.9.12.8.1362-4601e39. This all went well except that a large amount of my videos are no longer playing. These all worked fine as my wife pretty much streams West Wing day and night to her iPad and can no longer do that. The Plex server says transcoding and buffering, the app just displays the waiting icon.

These videos are all ones that were ripped from DVD a few years ago and have always worked fine. Some videos (from less dubious sources) added recently seem to work okay.

Any ideas of what I can check?

Thanks