It really sounds like OS3.9 is NOT the cause of your grief, seriously.
Do you know what hacks and patches you're running?
Basically, they are either started from the scripts
s:user-startup
s:startup-sequence
or from the directory
sys:wbstartup
A default OS3.9 doesn't have anything much here, except
rawinfo, classact (I think?) and amidock
If changing prefs with the prefs program doesn't work, I suspect you're not using the default iprefs program, check for this in s:startup-sequence.
