I've been shooting some test footage using mlv_rec on a Canon Mk3 113 firmware. The build I am running is the 07/03/2014. I've noticed a problem with the MLV files and I couldn't find anyone else in the forum that seemed to be experiencing similar issues.
When I change a camera setting during recording (ISO or aperture) it seems to create a problem when it comes to converting to DNG using all of the current MLV conversion tools on both mac and windows. It kind of 'trips up' the converting program and causes it to stop making DNG's from the rest of the MLV at the point that the ISO or aperture adjustments were made.
Using MlRawViewer on mac I was able to skip past the point in the clip where the camera settings changed, but extracting a full usable take is not possible. If I do not adjust any camera settings during recording I can shoot any length of clip my card allows and convert to DNG with no problems. I have tested many times and it is definitely the change in camera settings that causes this. Does anyone else have this problem?
I can confirm this issue. I thought I was going crazy! If you change the shutter speed, ISO or WB during mlv recording then the resulting file will be corrupt. You can test for this by playing back in camera where playback freezes on the frame where the settings were changed, giving the message:
frame and block size mismatch: 0x375F00 0x23A9AB 0x376EB4
(for example)
None of the conversion applications can convert these files. Here's an error message from MLVBrowseSharp:

I did notice that this issue doesn't exist in the Feb 23rd build, but does appear from Feb 24th onwards. Hope that is helpful. Keep up the good work!