I find it funny that Apple is the one in charge of the app store and they handle all transactions for developers. Which in turn means that they also control the app store. Since app developers submit to them and they are the ones that make the app available through the app store to everyone on the app store. So them saying that they can't do anything to help is mind blowing to me.
I would imagine it should be easy for them to figure out why you started receiving this app update, since this is their own system. My guess is that Apple doesn't want to admit to something being wrong in the app store that only affects a small user base.
The only other thing I can think of is that maybe someone in your household has the app and synced with your iTunes and some how that has flagged the app on your account.