I'm having this problem on AA trying to book a QR award. AA won't let me book my desired Flight 1 connecting to Flight 2, despite it showing as available on AA website. Get "We're sorry but at least one of the flights or fares you chose is no longer available.".
If I try to book Flight 1 -> Flight 3, or Flight 4 - Flight 2, both of those work i.e. all the individual flights are bookable but AA's website is not allowing booking of certain combinations for no obvious reason (despite the AA site showing the combinations as available).
I guess I need to phone to book.