Well think I have found the problem
Mkelley was right about the audio delay - this seems to be the issue.
I generated several different MKV files, some from AnyDVD, some from Handbrake and some from DVDFab. All showed the same sync errors using the same DVD as the source (in this case StarWars)
My current set up is - WD Live TV box connected to LCD via HDMI and using an optical cable to connect the WD Live TV box to my surround sound system (rather an old one truth be told, it does not have any HDMI inputs too old for that) I have my WD Live TV set to output the audio as digital since I am including AC3 or DTS audio in all the MKV’s and want to get the full surround sound.
Here is the problem. Set WD Live TV audio to Digital Ouput, when you play a movie the TV displays English AC3 (Digital) and the surround sound box displays DolbyDigital. Unfortunately the sound is ever so slightly out of sync for some movies. Should mention that the sound is lagging behind the video picture and not the other way round as MKelley suggested. Suggests that it is the audio decoding that is taking slightly extra time.
Set the WD Live TV audio to Stereo Output, when you play a movie the TV displays English AC3 and the surround sound box displays PCM ProLogic II. BUT the sound is in perfect sync with the video.
So, which is to blame? the WD Live TV box and its digital setting, or the surround sound box and its decoding of the digital signal?
Any suggestions? My aim was to create a large archive on an external HD with all my movies in full format with their surround sound, but it is looking like either my setup or something else is now stopping this Having the sound reduced down to stereo and then converted to ProLogic II to me is really a backward step.
As I mentioned, some movies play perfectly, some do not. I wonder, are some more susceptible to the sync error? or as I know the film so well I am just picking up the sync errors?