I'm not desperate, I'm simply done screwing with it. I've put far more time and effort into this issue than what's documented in this thread. I stand by my assertion that NO software out there can rip this title to MKV with perfect playback. If it gets fixed, great. As I said, if this were ONE title I wouldn't be concerned about it but it's a BUNCH of Disney titles all with similar problems with ATMOS. I don't suspect it's going to be LESS of a problem going forward. Elby is the only one even taking this problem seriously. MakeMKV doesn't seem interested in fixing it. DVDFab clearly hasn't fixed it even though it seems slightly better with them than any other solution I've tried so far. But having audio completely disappear in the middle of the movie is not a working solution. And I'm quite frankly tired of working on this issue. Elby has what they need to work on it and troubleshoot it further. Pete and James can repro the issue. I've done enough on this foolish problem.
I'm sure, now that it can be reproduced, it will be fixed fast - that is assuming, that it can be fixed and is not an inherent problem when converting a time-stamp based format into a more or less index based one.
I understand the basic problem with these HD audio formats.
First there's a general problem with audio and video packets when concatenating multiple clips (Incredibles has a ton of those clip cuts).
A video frame has a duration of about 41.7ms, an AC3 audio frame has 32ms. Clearly they don't align nicely. If you take 3 digits into account (arbitrary choice), you'll get a perfect alignment (both an audio and a video frame finish at the same time) about every 13.3 seconds.
So every 13.3s would be an ideal place to cut clips - obviously that's not practical.
So you always end up with clips containing a number of video frames and some left-over audio from which you'd actually be playing only a fraction of the frame before the next audio frame comes along. They overlap 16ms on average.
The only way to deal with this when aligning that mess into a linear MKV file, is to throw away packets every now and then. If you don't, the left-overs will sum up and cause lip-sync errors further down (a lot of tools actually do just that - or rather don't).
CloneBD handles that nicely for AC3 and DTS, which is well understood, but now those nasty HD extensions pop in. There are certain dependencies between individual Atmos packets - no documentation to lay them out. So you can't just throw away packets at will.
I suppose, that's what Elby have to figure out now...