Basically I use the custom variable setting. Here are the relevant lines from my custom.el . I also included all my other custome variable org settings in case something was overriding the stamping...

 '(org-time-stamp-rounding-minutes 5)


 '(org-agenda-custom-commands (quote (("d" todo "DELEGATED" nil) ("c" todo "DONE|DEFERRED|CANCELLED" nil) ("w" todo "WAITING" nil) ("W" agenda "" ((org-agenda-ndays 21))) ("A" agenda "" ((org-agenda-skip-function (lambda nil (org-agenda-skip-entry-if (quote notregexp) "\\=.*\\[#A\\]"))) (o rg-agenda-ndays 1) (org-agenda-overriding-header "Today's Priority #A tasks: "))) ("u" alltodo "" ((org-agenda-skip-function (lambda nil (org-agenda-skip-entry-if (quote scheduled) (quote deadline) (quote regexp) "<[^>
]+>"))) (org-agenda-overriding-header "Unscheduled TODO entries: "))))))
 '(org-agenda-files (quote ("/users/jrobins/org/work.org" "/users/jrobins/org/todos.org")))
 '(org-agenda-ndays 7)
 '(org-agenda-show-all-dates t)
 '(org-agenda-skip-deadline-if-done t)
 '(org-agenda-skip-scheduled-if-done t)
 '(org-agenda-start-on-weekday nil)
 '(org-clock-into-drawer 2)
 '(org-cycle-include-plain-lists t)
 '(org-deadline-warning-days 14)
 '(org-display-custom-times t)
 '(org-drawers (quote ("PROPERTIES" "CLOCK")))
 '(org-emphasis-alist (quote (("*" bold "<b>" "</b>") ("/" italic "<i>" "</i>") ("#
" Highlight "" "") ("_" underline "<u>" "</u>") ("=" org-code "<code>" "</code>" verbatim) ("~" org-verbatim "" "" verbatim) ("+" format-font-lock-strikethru-face "<del>" "</del>"))))
 '(org-fast-tag-selection-single-key (quote expert))
 '(org-fontify-done-headline t)
 '(org-hide-emphasis-markers t)
 '(org-hide-leading-stars t)
 '(org-remember-store-without-prompt t)
 '(org-reverse-note-order t)
 '(org-tags-column -120)
 '(org-time-stamp-custom-formats (quote ("<%b/%d %a>" . "<WW %V.%w %I:%M %p>")))

 '(org-todo-keyword-faces (quote (("WIP" . yellow))))
 '(org-todo-keywords (quote ((sequence "TODO" "WIP" "DONE"))))