Despite all my googling telling me that the iso9660 spec requires that the order of the directories must be alphabetical, when you give the command mkisofs -J -R -pad -o ./to_burn.iso /foo it puts the directories on the disk in the same order you get from 'ls -U /foo'. I only noticed this because I have a portable CD player that plays mp3 discs, but you can verify this with 'iso-info -l -i ./to_burn.iso'. I believe that the LSN (logical sector number?) gives the order the data is on disk. 99.9% of computers don't care about the LSN order of the directories, my mp3 CD player does. There should be some way to tell mkisofs to sort the directories so that the LSN order agrees w/ the alphabetical order (or maybe some other order, like the -sort option for files).
Sorry, feature requests need to go upstream. http://cdrecord.berlios.de/old/private/cdrecord.html