Here are my 2 cents regarding this issue.
I came across this issue the same day I started my DNS-323 for the first tine (firmware 1.08). Or to be more precise the same day I RESTARTED my DNS-323, because everything was working fine after initial setup - fan stopped and started no problem.
It looks like after restart firmware 1.08 puts fan into low/high mode no matter what's configured. So my workaround is very simple. Whenever I restart my DNS I go to web interface, power settings, make sure that fan setting is still on OFF/LOW/HIGH and JUST PRESS Save Settings BUTTON. That's it! I do not touch anything else.
Right after that fan momentarily starts spinning on High and then stops. Works for me 100%.
q1)Do you have C1 revision?
q2)Anyone know if you still have to do this on the 1.10b5 firmware?
q3)Is there a way to control temps within command line on C1 revisions?
appreciate any help with this, as I dont want to fry my disks (again most above is ONLY C1 related)