Just an update, because people asked me to. Once I sent JetBlue an excel file with all my purchases that were more than 30 days old, they transferred me to a points specialist, who seems to have manually added about 2500 points (which, if I looked back, would be roughly what I am missing) to my account. So worth being on top of them if things don't seem to add up. I think I might have to do this every few months.