There is a serious software bug with Background Transcoding under specific circumstances (I reported on it already some time ago under AAF-problems: http://community.avid.com/forums/p/160143/808148.aspx#808148).
The problem arises if Media Creation settings uses separate disks for video and audio. In this case Transcode in Background assigns identical file names for the video file V1 and for the audio file A1, while audio file A2 has a different name.
As long as you work with this configuration (seperate disks for video and audio) there is no problem, as the two files with identical file names (V1 and A1) reside on different disk drives.
However, if you transfer your sequence (or clips) with AAF-export to a seperate application (e.g. DaVinci Resolve) with the inclusion of media files in a folder, AAF-export can only export V1 and A2, but not A1, as it cannot place two files with identical names in one folder.
I discussed this case very lengthy with Avid Support, and they have acknowledged this error, however, a bug number was not created by some unknown reason. In fact, I received a message, that the case has been closed.
Joachim