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If you look close they're a little different, the first is INSIDE the default install location for CiviCRM (sites/mysite/MODULES/civicrm.. while the second is outside that location (sites/mysite/FILES/...UPDATE You're right, I typed it wrong. edited now.
Tested as you suggest. After a new registration (online or offline) the {debug} from a confirmation email shows that both $participant_status_id and $participant_status are unset. After an offline status change is made, the confirmation email has the $participant_status_id from before the change, while $participant_status is still unset. One thing that might be at issue: In our setup "Use a confirmation screen?" is set to "No" because our events are free. Are these variable perhaps dependent on the confirmation screen being displayed? If so, they probably shouldn't be.
I see what you're referring to. It's on line 34 and if $participant_status isn't present it falls back on the $isOnWaitlist variable, but when I run {debug} in the template I have yet to see an instance when $participant_status is actually set. $isOnWaitlist is accurate but doesn't provide the specific status. It lumps people who are assigned to the waitlist and those awaiting approval together as "true". Could this be a bug that was fixed after 4.6.9? I can run an upgrade, but it will take a while, with testing and all.