Thanks for the suggestions.
To my knowledge, flac does not do what I need. I'm not comparing an original to an extracted version which is what flac will report against.
The shntool cmp mode is not much different from the standard cmp/fc command line utility. What I'm looking for is something that will show duplicate sample ranges, missing sample ranges, difference ranges, etc and the offset of the sync points where the differences are detected.
I need to diagnose errors in decoded DTS-MA tracks. I can digest the results to see if there is a difference in the LPCM produced but it would be useful to have the more detailed information so that I know if we are dropping frames, duplicating frames, putting frames out of order, etc. I have hex comparison tools but the files are so large that the tools break when loading the files and I don't want to split the files. Even using the graphical tools, visual inspection to locate duplicate, out-of-order, etc conditions is to laborious for the test set in use.
I'm really trying to not write something.