Wirelessly posted (BlackBerry: BlackBerry8530/5.0.0.1030 Profile/MIDP-2.1 Configuration/CLDC-1.1 VendorID/417)
I'm sorry for the trouble you are experiencing.
To prevent the possibility of recurrences, I suggest obtaining a frequent-flyer number directly from the airline before submitting the credit-card application. If you include your (already-obtained) FF number on the credit-card application, I think that there is less chance of shenanigans like this occurring.
And I would ask to speak with Chase's Fraud Department, to ensure that a proper investigation is taking place at Chase's end.