StartCalendarInterval
     This optional key causes the job to be started every calendar interval as
     specified. Missing arguments are considered to be wildcard. The semantics
     are much like crontab(5).  Unlike cron which skips job invocations when
     the computer is asleep, launchd will start the job the next time the com-
     puter wakes up.  If multiple intervals transpire before the computer is
     woken, those events will be coalesced into one event upon wake from
     sleep.

So it's redundant to ever manually run the periodic scripts - they already fix themselves. Of course, this only holds true on 10.4 and later. So, moral of the story: never run the periodic scripts manually in 10.4 and later. They can take care of themselves.