Hmmm. Guess there are more problems in the stream. FFmpeg can't read the stream for whatever reason. Only thing you can try now is another (newer) build of FFmpeg.
Download it here: http://ffmpeg.zeranoe.com/builds/
(32-bit Builds (Static) - Latest)
Search for the ffmpeg.exe in the downloaded zip and replace the one within the MCTV installation folder (tools/ffmpeg/) with this one (make a backup of the original one). Then try again to convert it. Maybe the devs of ffmpeg fixed this problem in a newer version.
Other than that, the only help I could give you is if you upload a sample of a broken recording somewhere. I could try other settings/tools but hope is low...
But first let's try a new ffmpeg version.