Which LRT mod are you running, the older one or h.sie's realistic repair times? h.sie doesn't have seemed to made any changed in the ship damage, (my ship wasn't any stronger than before) which seems to be what you're experiencing for some unknown reason. The mod itself does a lot of different things beyong making the repair times more realistic:
http://www.subsim.com/radioroom/showthread.php?t=174225