We booked a great tour of Egypt that included a super deal with free airfare from JFK (direct flight) to Cairo. Also, it is a direct flight to Cairo, which only Egyptair has.
However, we couldn't extend the flight booking to our nearby airport. So, I had to book flights that considered delay independent of the Egyptair flights. I had a companion certificate with Delta and got a great deal of flights from JAX to JFK.
Problem amounted to having to book hotel rooms on each end of the trip, adding hundreds of dollars. Also, the Egyptair flight is now delayed several hours (so we have almost a 24 hour delay in JFK going to Egypt.
The perils of a free cheap flight.