Something that I left out of from further updates to my original post around 10 years ago after I did the first non-affiliate trunk post on batlabs was that I forgot to update some findings discovered in reference to setting CONVERSATION TYPE in the TRUNKING PERSONALITY ADVANCED TAB.
When I ran my first tests on two 700/800 systems, TEMPE AZ and Arizona STATE UNIVERSITY back in the mid to early 2000 time frame, I experienced similar issues as yours and I was missing a fair amount of the comms even after alignment on 2 of my 3920's.
One thing that I did was to make 3 duplicate trunk personalities but ONE had the CONVERSATION TYPE set for PTT-ID, the 2nd set for TRANSMISSION and the 3rd for MESSAGE even though my radio didn't have a transmitter chain in it, the CONVERSATION TYPE, as I recall, had an effect on the receive end..
As I remember one of these personalities CONVERSATION TYPES resolved my issue but being that this was over 10 years ago in my case I don't remember which of the 3 CONVERSATION TYPES resolved it but it's worth a try to make 3 duplicate trunk personalities set to the 3 different CONVERSATION TYPES and test each one.