My problem is *also* on 10.8.5 (Mountain Lion)
2.1.0 & 2.1.2 tested as not working, but reverting back to 2.0.9 solved it for me.
Mostly it was .mkv & .avi files (single as well as inside splitted RAR)
According to JB, you need to unstack the windows... now where and how do I do that?
I've gone through all the right-clicks, the menu choices, the preferences, but I still don't see that myself ;(