Dave, I spent a bit of time testing this tonight and it is indeed a callsign issue.
If there
is one (a callsign, that is, e.g. Aegean, Speedbird, Shamrock etc. etc.), then the COM log shows the ATC text just fine. If there is no callsign however, so ATC just leaves it blank and reads back the flight number only (i.e. the value in the pf3_callsigns.dat file is 9999, 98) then no text appears in the COM log, as I suggested in my previous post here. I tried this with a number of airlines with and without callsigns programmed into in PF3 and it was true for every one. Callsign exists in PF3 = COM log working; Callsign absent in PF3 = no text in COM log. So if you choose 'None' in the callsign list, then there's no text in the COM log window.
I attach the log (I restarted PF3 between each test, so not sure how much useful information it gives).