Media Encoder 5.5 Watch Folder Outputs

Since upgrading to CS5.5 I've noticed a strange occurrence with watch folders. In CS5, source files would all be put into one "Source" folder. But now Media Encoder is putting each individual file into its own timestamped folder within the Source folder (See image for a better explanation).

I've searched around but cant seem to find reference to it anywhere (even in the Adobe manuals / help sites)

I know I can do a find all to grab all the movie files and put them back into one folder but is there any way to prevent this from happening?

(I assume the purpose is so that you have a record of when a particular file was encoded, however for our workflow (dealing with hundreds of files on a ftp server each day) its somewhat annoying. )

Using Adobe Media Encoder 5.5.1.12 (64-bit) on a Mac Pro running 10.6.8

Did you ever get this problem solved?