first of all you may not use a simple ".." to indicate the parent directory. then, when using something like [open_basedir = .:../x:../y] it will work, but not only for "../x" and "../y" but also for "../z" if you try to give more than 4 parameters (this all running on freebsd 3.0) all your php3.ini settings will be droped and the default settings used.

my php3.ini file:
---------------------------------------------------------------------
safe_mode       =       On
safe_mode_exec_dir      =       /nonexistent
open_basedir    =       .:../admin:../php:../php3
upload_tmp_dir  =       ../tmp

;error_log      =       syslog
;short_open_tag =       on
---------------------------------------------------------------------

i saw configuration settings also being reset when short_open_tag was set to on.