Make sure the saved settings are in SYS:Prefs/Env-Archive/Time.prefs (or ENVARC:Time.prefs if you know your assigns ;-) )
It might be (but highly unlikely) that it's saving the prefs into ENV: instead of ENVARC:
Failing that boot from the Emergency disk and change and save the prefs on that then reboot. If that works, copy DF0:Prefs/Env-Arhive/Time.prefs to SYS:Prefs/Env-Archive/Time.prefs then reboot from your HD and see if that's worked.
These are the only two things I can suggest. Hope it helps.
