Depending on how you mounted 3.9 CD for install the files are write protected
type in shell:
cd sys
refs/env-archive/sys
list
here the files should have ----rwed or ----rw-d
if not type:
protect #?.prefs wd
or for all files
protect #? wd
hope this helps you
EDIT:test that first and now i'm 10 mins too late