My understanding is that the madVR measured refresh rate is always the same for Jong, namely 50.0011, with both DVD and VOB playback. I don't think it is likely that madVR is not reporting this properly to VideoClock. I believe the problem is likely to be somewhere else...
The difference between DVD and VOB playback for Jong seems to be the audio clock deviation. If VideoClock is doing it's job, it should notice that the refresh rate is too high and should consequently speed up the audio master clock, too, by the same factor. If VideoClock is doing that, madVR's "deviation" measurement should show that. According to Jong this does happen with VOB playback. There audio clock deviation is measured by madVR with 0.0022% which is exactly what is needed to "fix" the too high video refresh rate. However, with DVD playback it seems that VideoClock is not speeding the audio clock up at all. madVR measures a audio clock deviation of zero. As a result madVR has to repeat frames.
@SBR, the latest madVR version v0.85.8 has a new "repeated frames" counter in the OSD which counts repeated frames due to a mismatch between movie framerate and video refresh rate. And this counter actually goes up for Jong (it does, doesn't in, Jong?), in accordance to what the "frame repeats per minute" estimate suggests. So there is a real problem here.