hi everyone,
I ran into this a while back, here is the soluton, it works great for me on 5.6
1. copy the template 40IBayAccess
from /etc/e-smith/templates/etc/proftpd.conf
to /etc/e-smith/templates-custom/etc/proftpd.conf
2. add this line
$OUT .= " AllowChmod on\n";
above $OUT .= " AllowOverwrite on\n";
and below $OUT .= "<Directory

/home/e-smith/files/ibays/$key/*>\n";
3. expand the template /sbin/e-smith/expand-template /etc/proftpd.conf
you are done. this allows chmod capabilites for every ibay that you create.