The manual says (under transferring wave files from computer to RC-300)
Do not place more than one WAV file in any folder. If a folder
already contains a WAV file, do not overwrite it. Write your WAV
files into empty folders.

Seems like a pretty restricting rule for the RC-300, when used as described in OP.
BiaB can't make it change folders for each wave. I think the unit is meant for 'one at a time' transfers.

http://www.bossus.com/backstage/product_manuals/?group=2

Around page 36


Make your sound your own!
.. I do not work here, but the benefits are still awesome