It is common building practice to use flashing to keep moisture from getting between the house and the ledger. The Uniform Building Code requires flashing, and many contractors meet the requirement by installing an L-shaped piece of metal. The horizontal leg covers the top of the ledger and the vertical leg goes up the wall and is lapped by the building paper and siding above.
Most carpenters install the ledger in the same plane as the joists, so the deck surface ends up an inch or more higher than the horizontal leg of the flashing. This creates a perfect collection zone because if something falls in toward the house, the flashing will prevent it from falling through to the ground. If enough organic matter collects on the flashing, it can induce rot in the adjoining deck board or invade the siding above.
The simplest way to deal with this problem is to use a ledger that is taller than the joists and install it so the top edge will be in the same plane as the deck boards once those are installed.
You still need to flash the connection, but the flashing should come down the wall from behind the siding and building paper, run across the top of the ledger, and end in a lip that laps down the face (see illustration below). —Adapted from “Rot Resistant Deck Details,” by Kim Katwijk, which first appeared in the April 2005 issue of THE JOURNAL OF LIGHT CONSTRUCTION (www.jlconline.com), a sister publication to REPLACEMENT CONTRACTOR.