Apologies for the delay incoming back on this, I've been busy away from the FS world
Anyway, here are a few thoughts (I'm aware that you have also been posting re the new flight plan processing):
Although there are multiple ways of calculating a flight plan profile, the only one that matters is the FMC - it uses real-time data during the actual flight, including the actual groundspeed and weather conditions. Any calculation made by LNM is based on on the aircraft performance profile used.
PF3 calculates a TOD based on 3nm/1000 feet from the cruise altitude to the FAF - this can now be altered to 4nm or 5nm using the descent option in Options 2/Advanced:
2024-01-21 18_44_48-.png (14.44 KiB) Viewed 10967 times
(Dave will, I'm sure, correct me if I'm wrong but I understand that the PF3 aircraft profile only affects the VS speed set if in VCP mode 3.)
I have found that for a 737-600, my default airliner, the 'medium' option works best - you may care to try 'medium' or 'long' to see if that works for you.
Cheers,
Martin