This is driving me nuts and I can't find any direct solution to the problem, so I'm going to try and ask the question a little different than the OP. (Same issue as OP)
Is there a way in iTunes to not automatically sync every fricking app that is in my iTunes library??? Everytime I try to sync my iPhone, hundreds of apps, all of which are in my iTunes Library (Not New Apps) on my mac try to sync to my phone, which can't store them all even if I wanted to install all of them. This prevents me from installing old backups and from installing software updates properly if my phone is near max capacity for space.
iTunes has options to only add music and videos manually or from checked selections, so why are the Apps automatic no matter what I select in App options?