. . . . The Microsoft converter to a dvr-ms file doesn't work with long files . . . .
There is no file length limitation on converting WTV to DVR-MS with the MS converter.
.Does the MS converter fail on other recorded files?
Converting to DVR-MS may not work because it is a propriety Microsoft format not supported by MEP 17.
There are several third party converters available which will convert WTV to other MEP supported formats, however if the MS converter falls over with the video they are likely to as well.