Do I recall correctly that this Mod was originally for Multiplayer?
What was done to a crap load of Ships was the cfg#FLG node was renamed to cfg#F01
Then an entry was added to the ships eqp file for the flag.
Should you try the clone I showed s7rikeback you'll see no flags!!
I can do a mass rename and write something to adjust the eqp files in mass also.
It's gonna take a few days to correct this.
Mostly because I work 10 hours a day at my real job.