To solve this I used to run a little script that would use DVR2WMV to transcode all the files in the Recorded TV folder to WMV and remove the DVR-MS files. This was causing more and more issues, like sound dropping out and files becoming corrupt.
To solve the problem I looked into some other tools and found AutoDVRconvert on the "The Green Button" forums, and this tools seems to do the trick. It can do conversion to WMV and MPG. Not only does this tool work better, it also seems to run much faster, 5 minutes for an hour of video.
The install was causing some problems for me, and the documentation was not very clear so I'll explain.
- Download AutoDVRconvert
- Extract all the files to the Recorded TV folder, in my case "D:\Recorded TV"
- Run register filters.bat in the Recorded TV folder
- Start AutoDVRconvert and set up an input and output folder
You could configure AutoDVRconvert to delete the original if the conversion was succesful, I'm only going to do this when I am sure everything works fine.