I was just wondering, when one of my Galaxy Class is under attack and I seperate it - the saucer shares the same damage as the stardrive. I.e. If the engines are down when the ship seperate both units are disabled. Is this hard coded or can it be altered that once seperated; your saucer section can escape. After all that's what would happen in the movies and is the point of saucer seperation!
The only thing I can think of is try editting the saucer section's odf so it has more engine's hitpoints, see if it works.