Did you check for codec problems using filmerit?
I am not that familiar with it myself, but I know my collegue Paranoid Delusion believes in it so then it MUST work
It hadnt fixed the issue however I have now found the cause. It appears that when I copy the files from my PC (which works) to the HTPC something corrupts. Tried downloading the files directly from the HTPC and they work. Then downloaded robocopy and used that and all seems fine.
Thankyou for everyones input and suggestions, much appreciated.
Did you try to remux your file with MKV merge? This will detect/fix problems in video file.
You should try to play your file directly in Graphstudio to eliminate player problem.
If you have SAF6 installed, you can find graphstudio START-SAF-Tools-Graphstudio.