Here's a not very satisfactory workaround. You can play an episode in your browser, copy the URL, then go to StreamFab and add it to your queue for download. You have to do it 1 episode at a time, beause the name in the queue will be the series name only. It adds Title, Year and Genre tags, but the Title is just the series name. It adds a black rectangle for cover art, but not the correct cover art. The filename is just the series name, so you need to rename each downloaded file to keep track of which episode it is. As I said, not a very satisfactory workaround, but if you really need an episode other than episode 1, that's how you can do it. You probably have to start playing the episode in your browser to get the correct episode. When I simply selected an episode without also clicking Play, I ended up with episode 1 even though it was episode 3 of the season. I was able to get episode 3 when I clicked Play before going to StreamFab to add it to the queue.
This is a critical issue for Amazon downloaders, and I hope StreamFab releases a fix for version 6.1.6.7 (the last without re-encoding) as well as for 6.1.7.3. Better yet, drop the re-encoding altogether. But if they keep re-encoding, they need to fork the code and release 2 new versions with a fix for this Amazon issue.
