Well, this one "re-encoded Lavf56.1.0: handbrake mkv 37.6 MB" also plays fine using the "old" ffdshow codecs.
But unfortunately it seems to be a progressive coded sample as opposed to the interlaced coding of your original sample.
Probably more useful to stay with interlaced AVC samples?
One thing that does kind of seem odd is:
I thought that AVC uses MBAFF for interlaced content and Mediainfo normally picks that scan type.
But with your original sample it shows the AVC as having a scan type of "interlaced" in lieu of "MBAFF".
Not sure if setting the fake interlacing flag would present it that way?
Not done much AVC encoding so no experience with that (I think the faking is used for segmented progressive frames?

)
I think only mean has the expertise to find out what/where some deleterious change has snuck in.