Hmm, interesting ... we were kinda scratching our heads on why some stuff worked in hb and some stuff didn't. MakeMkv seems to be the culprit possibly ?
I certainly am no expert when it comes to this stuff. I'm sure you've seen me post plenty of silly questions over on the handbrake forums, but I have done a lot of messing around with MakeMKV and so I have noticed a few trends, and I can comfirm that there is something strange going on with the mkv files produced by MakeMKV.
First of all, Handbrake seems to strugle with MakeMKV produced mkv files if they contain PGS subtitles. The vast majority of mkv files that I've produced with PGS subtitles in them seem result in Handbrake saying "No valid source". I don't have any logs handy at the moment, but I can certainly do a few tests to verify this. My experience though is that PGS tracks will 4 out of 5 times cause problems.
Another thing I've noticed is that a few of my MakeMKV rips end up with strange fps. I have a norwegian movie series called Varg Veum on BD. According to VLC, the original m2ts files contain a VC-1 file encoded at 25fps. According to the log, Handbrake also determines it to be 25 fps. If, on the other hand I use MakeMKV to produce a mkv file, the handbrake log suddenly reports it as being 50fps. Another interesting thing is that the ETA while encoding this MKV is completely off. For some reason the percentage complete is 1/2 of what it actually is, so when it reaches 50%, it's suddenly done and I end up with a perfectly functioning file. I havn't reported this on the handbrake forum yet as I'm on a different computer at the moment (work computer), but I used Quicktime to record the ETA bar as it reaces 50% showing the effect. i'll post a link to the screencast and post the log on the handbrake forums later tonight if it hasn't already been reported. This problem does not exist when using the original m2ts file from the BD.
Another problem with MakeMKV has to do with autocropping in handbrake. When I load the mkv into handbrake, I often find that it's unable to do an autocrop because the video in the preview is completely scrambled (covered in gray boxes). This only happens with mkv files from BD disks as far as I can tell as I also tested this on a few DVD's. This hasn't happened on any of the m2ts files I've tested.
I'm really fed up with makeMKV. At the moment I'm only using it to rip a backup of the BD disk and then I use handbrake to encode the m2ts file. This seems to work problem free every time. The only downside is that I'm left without chapter markers which is a shame. I really hope that someone adds support in handbrake for reading the mpls file. Then there would be no need for us to use MakeMKV as Handbrake could read the chapter markers from the mplis file and, once support for pgs arrives, also find the subtitle tracks. I'm dying for a reason to get rid of MakeMKV.