The money from your bank account (-1000) is actually a transfer to your mortgage co (+1000) then the mortgage company actually applies the funds to the correct expense ( - interest, - principal, - escow account) I am not sure if you are seeing these transactions in your mortgage account.
I said technically, because while correct it is annoying and not data I choose to track. instead, I only mark the one item out of my checking as Mortgage. I then create a new category called Mortgage Details (type = Transfer) and categorize all of the other mortgage transactions with that one. Since the category is a transfer, the cash flow reports just ignore them, and the cash flow now looks correct.