I'm not really sure I know a good way to share one of these files as they are many GB bluray rips.
However, I think I have a lead: the files that fail all have in common that they are MKV containers with A_DTS audio tracks at 48k sampling frequency, 6 channels, and 24 bit depth. I'm thinking something about the format (particularly the 24-bit depth) might not be read properly when analyzing the audio. Interestingly, if I transcode these files in JRiver to MKV H264/AAC 1080p, they transcode fine and the converted audio also scans with no issues. If I try to transcode *just* the audio to FLAC, it fails (I'm not sure how to actually see logs from that process).