the problem only occurs with callsigns starting with letters
Not quite sure what you mean by that - all call signs start with letters ('Speedbird' starts with 'S')..

Presumably you mean when the
flight number is in letters (?).
It could be that a lot of my aircraft.cfg files (the AI ones, I mean) do not have the correct atc_airline or possibly any entry at all for atc_flight_number. If PF3 ultimately gets the data from the aircraft.cfg file, that could be a reason for the problem. It would be a HUGE job to correct all these, so I wouldn't attempt it unless it is sure that PF3 is getting its data from the AI aircraft.cfg files (via FSUIPC). Begs the question, where does FSUIPC get its call sign data from?
On the other hand, for user aircraft, call signs must be pre-programmed into PF3 and are selected automatically when you choose the airline in Options #1. Whatever is in the aircraft.cfg file is ignored, as far as I can tell.
I attach my log, which of course I am unable to read.
Thanks.