Here's how Expedia replied to an e-mailed question on this:
We have two types of hotel reservations on Expedia.com. We have regular hotel reservations, and Expedia Special Rate reservations.
For regular hotel reservations, Expedia does not make any charges to your card. We submit the credit card information to the hotel/property for the purpose of reservation, and the hotel/property will be the one to charge you directly. For this type of hotel reservation on Expedia, you may receive corresponding award points for the hotel whenever applicable.
For Expedia Special Rate reservations, Expedia will be the one to charge your card. Every Expedia Special Rate Hotel reservation is guaranteed to be the lowest rate available online at the time of booking. It has a "Low Price Guarantee." (We will match the price on competitors’ Web sites for the same hotel, room type, and dates of travel if we are notified within 24 hours of your room purchase on Expedia.com.) Expedia has negotiated with the major hotel chains in order to offer our members incredible savings on our Expedia Special Rate hotels. But along with these savings come several restrictions that were explained to you along the purchase path. One of them is that "Award points and airline mileage may not be awarded when booking an Expedia Special Rate hotel."
This is consistent with what
Starwood Lurker posted above. It boils down to this: if you pay a published rate, you get miles/points. If you get a special rate, you
may have to forego them. Limiting the "special rate" category to opaque sites in my earlier post was too narrow. Some special rates, which don't earn miles, are transparent.