Ive booked most of my hotel stays at Hilton at Expedia. My points have been showing up nice and regular.
Once when I found a lower rate on Expedia than on Hilton, I called the reservation agent who was quite nice and told me she couldn't match the rate, just book away on Expedia. The other strange quirk I've had is I have been told that the rooms are "sold out" on Hilton and they show up on Expedia. I booked one, they gave me a conf #, I put down a deposit to make sure, and my stay was just wonderful.
The only upside I've found for booking in directly at the Hilton Res Computer system is you can do a zip check in where you don't need to do anything. I check both prices either way. Part of it could be I usually end up with the AA discount on expedia, or specially negotiated rates, where I don't know which code to enter in hiltons reservation system for AA member discount.
VizSFO