www.makemkv.com

Nevermind, I was forgetting to open the tree file options on the individual files, and the hd audio was not selected as default.

Everything I have read suggests that the latest versions of makemkv preserve hd audio tracks and produce mkvs with dts-hd or dolby true hd. And I don't see any options in the program to do otherwise. However, I have made backups of several retail bluray discs recently, most with dts-hd audio tracks,...