Hi Jim,
In that case I would suggest one of:
1) Activate the Mythbuntu PPA and get to current .25-fixes. You are on .25.2, which is pretty old. Since this is not a problem we frequently hear of any more, the very first thing you should try is this (which can/should hopefully also get you a more up to date libx264).
2) Get your Mythbuntu upgraded to a .26 version, which is the current release version of Myth.
3) Compile a current libx264 and then compile current myth against it.
Listed in increasing order of difficulty, but also increasing liklihood of success. Unfortunately the app really has no control over the backend providing poorly transcoded video-- I suspect step "1" will be enough to get you sorted out, and if not, step 2 almost certainly should.
Robert