This has happened to me as well. I was flying A->C with a connection in B. My B->C flight credited just fine, but my A->B flight didn't post. Called AA, who at first told me I was a no show at airport A.

I then asked, "well, if I actually was a no-show, then my ticket would have been cancelled when I missed my first flight, right? Then how the heck did I manage to get on my second flight on the itinerary??" After a series of escalations and holds, I was given a similar story as yours: my ticket was "open" and somehow there was no record of me being on the first flight. So I had to send in my boarding pass for research. This was just before the systems merger, on AA ticket stock flying US metal. Further slap in the face when I was told that instead of the normal couple week turnaround for AA miles to post, I had to wait up to 2 months, as "US Airways is a partner airline and not formally part of AA yet."