Just trying to help so you know why this is happening. Below I'm quoting some stuff from how we got the other program to week with every file. Most people that download ps3 media server aren't going to mess with all these config files. I hope this will help for an end solution...
Transcoding on-the-fly is a very delicate operation because the transcoder has to process every frame that it handles and is therefore normally only a few seconds ahead of the play head on your device. The MPEG-PS container allows the device to start playing the movie, even though we are still transcoding. If this did not happen you would have a 1 or 2 hour wait before the movie started due to us having to wait until the whole transcode finished.
In all the logs that I have seen from Visio customers, the TV requests a few chunks of data right at the start of the file which kicks the transcode process off. After a few seconds it then requests a chunk of data right from the very end of the file! at this point we say that we cannot possibly service that request because the transcoder is nowhere near that point of the file and the wait time would be large.
All other devices Sony, Samsung etc. etc. request small, incremental chunks of data that are always behind the transcoder write head, meaning that we can always service that request. We have a spoofing mechanism in place that just generates random data when the device requests it at the end of the file and I think that it is this random data that is causing the issue.
The mechanic of the streaming is what is breaking the transcoding, not the actual format of the files.
Vizio is not the only ones who act like this, there are a couple more but, the vast majority behave correctly. That is why we built the 'back door' into the tvmobili media server for clients that do behave this way.