In my experience with down-converted TrueHD->AC3 titles (all using TSmuxer).. Handbrake does recognize and encode them.. but it takes it a very long time to scan the files, somewhere around 30-45 minutes. Just start Handbrake and go do something else, and you will see it will eventually accept the title. I am using released 0.93 version.
I tried that last night, and woke up this morning to see that in finally finished scanning the file.
Unfortunately, it was encoding at 2 FPS on my 2.0Ghz Core 2 Duo MacBook. I finally stopped it after two hours. It just wasn't worth it when Visual Hub could do the entire file in 4 hours. However, Handbrake's encoding quality is so much better.
I'll wait for the next snapshot before trying again.