@mitu @GoldManSex778 - Thanks for the advice. I converted with handbrake, basically opened the video in h/b and ran it through without messing around with the settings.
Now both the portrait and landscape videos display with the correct aspect ratio and work with omxplayer
Thanks so much.

@greenhawk84 I'm mostly talking about editing the file itself, as long as you edit the metadata through the ES editor that's fine. Post the gamelist file on pastebin.com if you don't find the culprit , so we can have a look.