I just created my first data disk with brasero/bonfire 0.5.2 (without beagle/libburn support) and had an unexpected result.
I dragged several folders to the disk compilation and was seeing an nice folder hierarchy, but when I had burned the disk the top level folders were missing - their contents were directly on the cd.
First I thought it was a major bug and therefore tried to make a compilation by hand with mkisofs. I gave all folders I wanted on the cd as argument to mkisofs - and I got the same result as with brasero.
So I first concluded that brasero uses mkisofs and second that it passes the folders as arguments as I did. Probably one would have to use -graft-points to fix this behaviour.
And in my opinion this should be fixed because it's quite unintuitive - not only because it's different from what other programs do, but it also contradicts the WYSIWYG paradigm.