This is just a thought, but especially with Entrenchment, there is the need to update or change any entity files added to the gameInfo folder. say i take a scout and make a scout2. In scout2 i change some of the settings. Weapons or hull or shields.
If i simply save and exit and start Sins and load the mod, the mod will cause the game to mini-dump. Many times i dont know this until i get out and see the error on the screen.
But the reason is i didnt update the entity.manifest file for the file i added.
But if i go into the manifest (open with notepad) and go down to frigatescout and copy, press enter for a new line
click paste and change the now second line which has scout to scout2 then go to the top, change the number of entities to 1 more than what it currently is, then i save and exit, start Sins and load the mod. Usually, if i haven't missed something else, im now ok and the mod will play.
Just a thought, this might not be the case at all if you havent' added files. 
-Teal