So what's the answer here. I'm having the same problem. The only differance is I'm programatically setting the path.
ceMaintenance.Setting("security:ImageGalleryPath") = "~/images_customer/" & Session("EmployerID")
ceMaintenance.Setting("security:MediaGalleryPath") = "~/images_customer/" & Session("EmployerID")
ceMaintenance.Setting("security:FlashGalleryPath") = "~/images_customer/" & Session("EmployerID")
ceMaintenance.Setting("security:FilesGallaryPath") = "~/images_customer/" & Session("EmployerID")
None of these seem to have any affect on the Downloadable Files path.