www.makemkv.com

This problem (no commentary audio extracted) happens on any of the Fringe DVDs that contains a Commentary track.

None of the tracks contain more than one English Audio Track.
All of the MKV titles produced only contain one audio track (the main one).

Note in the log below the line "Title 7 in VTS 1 is equal to title 5 and was skipped" this seems to be the video track with the "Commentary track".
Why does MakeMKV think it is the same?

Is there a way to force MakeMKV to not skip what it thinks are duplicates because then I could extract the commentary track from it?

This log is from Fringe Season 3 Disc 5

Using direct disc access mode
Title #0 was added (35 cell(s), 2:53:35)
Title #2 was added (8 cell(s), 0:43:45)
Title #3 was added (8 cell(s), 0:43:05)
Title #4 was added (8 cell(s), 0:43:51)
Title #5 was added (8 cell(s), 0:42:54)
Title #6 was added (8 cell(s), 0:43:51)
Title #7 was added (1 cell(s), 0:07:30)
Title #8 was added (1 cell(s), 0:00:10)
Title #9 was added (1 cell(s), 0:00:12)
Title 7 in VTS 1 is equal to title 5 and was skipped
Operation successfully completed
Saving 7 titles into directory Y:/Video/FRINGE_SEASON_3_DISC_5
7 titles saved

The attached zip file includes the *.IFO's and the debug log file as per the FAQ #8 instructions http://www.makemkv.com/faq/item/8

The episode titled "Lysergic Acid Diethylamide" is the one with the Commentary track.

I have saved the entire DVD in case you need any further files from it to help solve this issue.

I have submitted this to support@makemkv.com on Dec 7th but have received no response as to if it was received.
So I am posting it here to see if this problem can be solved.

You won't receive a response unless the developer needs more information from you in order to fix the issue.

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Dedicated Rip Box: Assassin HTPC, XBMCbuntu 12.0 (Frodo), Intel i5 3570k 3.4 GHz Ivy Bridge w/ HD 4000, LG BD-ROM
Playback Devices: MyGica EnjoyTV 120, Xtreamer SideWinder 3, Crystal Acoustics MediaMatchBox, Google Nexus 4

Well a response that the files were received and that they were looking into the problem would have been nice.

Don't shoot the messenger. I'm just telling you what I've learned from experience. I've never been contacted by support unless they have needed more information. Personally I'd rather they spent their time working on the software than sending out thank you emails.

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Dedicated Rip Box: Assassin HTPC, XBMCbuntu 12.0 (Frodo), Intel i5 3570k 3.4 GHz Ivy Bridge w/ HD 4000, LG BD-ROM
Playback Devices: MyGica EnjoyTV 120, Xtreamer SideWinder 3, Crystal Acoustics MediaMatchBox, Google Nexus 4

Where did I ask for a thank you?

For all I know I sent the files to an email address that wasn't monitored.

Heck even a robo-response would have been better than complete silence.

It sure would be nice if they had a bug tracking system so that we would know that the problems we report have been identified and that someday they might be fixed.

Right now I have no idea if any of the software programmers are even aware of this problem.

This is a bug in MakeMKV. You are right, the skipped "title 7" is a copy of episode 3 , and the only episode with a commentary track. The bug in duplication logic will be fixed in the next version. The really right way to fix this bug is to recognize these two titles and merge them into a single title with both audio tracks. It's unlikely that this will be done in the next version.

As for communication, response by crowfax was very accurate.

MakeMKV v1.7.1 has partially fixed this problem for the Fringe DVD's.

The Episodes that have a commentary track are not merged into a single MKV file with both the primary audio track and the commentary track as expected. What is produced are two different MKV files where both have the same video track but one contains the primary audio track and the other contains the commentary track.

In order to produce the proper single MKV file with both audio tracks I have to use mkvmerge and add the first MKV which contains the video and primary audio track and then add the second MKV that contains the commentary track. I then uncheck the video track from the second added MKV and then remux.

The above workaround gets the proper result but will a future MakeMKV fix this issue so that the workaround will no longer be needed?

It's possible the DVDs were authored this way - with the main audio and commentary audio found on two different titles. It's not common, but I've heard of it on a couple occasions.

The Claymore box set is like this.

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Dedicated Rip Box: Assassin HTPC, XBMCbuntu 12.0 (Frodo), Intel i5 3570k 3.4 GHz Ivy Bridge w/ HD 4000, LG BD-ROM
Playback Devices: MyGica EnjoyTV 120, Xtreamer SideWinder 3, Crystal Acoustics MediaMatchBox, Google Nexus 4

It would be nice if MakeMKV would see that the it was going to produce two separate MKV's that had the same video track but different audio tracks to get around these problems.

When this problem was first reported MakeMKV detected that two video files were the same and excluded the second one. The first had the primary audio track and the second had the commentary. So MakeMKV has logic to detect when video tracks are the same.

So why can't the fix be as easy as detecting the two equal video tracks (already in MakeMKV) with different audio tracks and produce a single MKV with both audio tracks?

Actually, I missed this when I replied to you: