Just wanted to give an update.
First off, thanks for the support/sympathy.
Unfortunately, the issue remains largely unresolved. While my account has been properly credited, my traveling companions are still missing large chunks of TrueBlue points.
Since I first posted, I've followed up with JetBlue twice. What's puzzling about this issue -- both to me and to JetBlue -- is that the errors in crediting the points are largely inconsistent.
To give a recap of the situation: I flew roundtrip from JFK to SJU in August, with 4 family members on the same itinerary. Two of us had previously flown JetBlue and gave our TrueBlue numbers when booking. The three others were flying JetBlue for the first time. After the flights were completed, each of them registered with TrueBlue and submitted a missing points request. As I noted in my original post, my points did not post correctly -- even though I had given my TB number. I was missing the bonus points (see my original post in the thread for an explanation). That issue was resolved for me and for my traveling companion who already had a TB number.
What is really bizarre is what happened with the accounts of the three flyers who joined TB after our flights. Each of them is missing segments and/or online bonus points. Yet they're not all missing the same points. Some have them for the flight out of JFK but not for the flight back. Some have bonus points while others' remain uncredited.
In speaking with customer service representatives and even a TB supervisor, I was told that I may have to wait several weeks for the issue to be resolved. Again, I was told that the new database/reservations system continues to be problematic. They were good enough to send e-mails to the appropriate departments (IT? TB?) to try to get the issue resolved, but all of us were planning on using those points for travel in the near future -- points that we earned but haven't received. Since the point cost of a flight varies much like the dollar cost does, it would be ideal to have those points ASAP.
All in all, I'm thoroughly disappointed by the entire situation. I've never had such a hassle when trying to get FF miles credited, and I can't believe the computer system JetBlue uses seems so buggy.
Any advice on how to proceed, or whether I could get compensated for having to wait so long for my points, is appreciated.