WELL I'LL BE DAMNED.
I check this thread every day. Finally progress!!!
So after reading the posts above I got all excited, went to try my 2 missing flights.
Garuda - no dice. However! Progress. I went from "oops theres something wrong" and "no points were claimed" to (paraphrase) "the airline needs more information about your flight" and the REAL manual claim process as opposed to just the email process. So, resolved? Not by a long shot, but PROGRESS!!!!!
Virgin - HUZZAH! Previously I was at "airline requests more information" and manual processing. This time, "your points have been registered!" only to not see the balance go up. But, then I went back to the home page and navigated in to the profile again and poof! New York to London 864 points!
So now I'm at 14/15 airlines. Huge fist pump. Progress feels good

Now lemme go update that damn spreadsheet!