DSM-G600, DNS-3xx and NSA-220 Hack Forum

My Setup:
#DNS 323; 2x 1Gb HDD without raid; 1.09 firmware.

What I usually do:
#1 - Install ffp (0.5), activate ssh
#2 - Create a couple users, and a group.
#2 - Install sudo package (and sudoer myself)
#4 - Change user rights on drive to manage who has what rights on which files via linux. Create 1 single "top level" samba share.
#5 - Usermod my users to -s /ffp/bin/sh -d /ffp/home/USERNAME
#6 - Create some ftp shares
#7 - Other?

What happens:
The machine decides "something" is wrong and proceeds to chmod the entire drive! This happens when the machine starts up. This is especially frustrating for 2 reasons:
#1 - Completely messes up ffp and ssh (ssh refuses to start because the keys are public)
#2 - My girlfriend backs up her entire development machine on my NAS, so it's about 500 000 files. It takes hours to undo the damage...

The question
Does anybody know what I am doing wrong? At what point does the firmware decide that my drive needs its rights reset? Are there any "Do nots" or "Do not touch files" I should know about? I haven't been able to pin down what is triggering this, and it's driving me crazy!

Thanks for any input.