I have had the following happen to me twice in 3 months. I reserve a flight on delta.com, and find (after arriving at airport) that all my flights on my domestic itinerary have been flagged with "declined elite upgrade". After hours on the phone with delta, they finally sent an email explaining they do this on purpose. This happens if you 1. don't log in before searching for a flight, 2. come to delta.com through kayak or similar, or 3.book a trip through a saved trip template. This seems incredibly stupid:

Dear Sir,

Thank you for contacting Delta Air Lines.

We are truly sorry for the frustration and inconvenience you experienced
concerning your complimentary Elite upgrade.

We contacted our delta.com team and were able to identify three possible
causes that some elite-level SkyMiles members’ Complimentary Medallion
Upgrades are not being automatically requested at the time of booking,
or are being declined in error.

First possible cause, the customer is not logging-in to delta.com prior
to beginning their flight search. If the customer waits to login after
selecting their flights, their upgrades will be declined automatically.
This is one more reason to encourage our elite customers to login
immediately upon accessing delta.com.

Second possible cause, the customer is using a 3rd party travel web
site. Sites such as www.kayak.com allow customers to shop and select
their flights before redirecting the customer to the airline’s web site
to complete their purchase transaction. When Medallion customers do
this, their upgrades are automatically declined during the transition
from the 3rd-party site to delta.com because the flights have already
been selected.

Lastly, the customer is using a saved trip template which specifies “no
upgrade.” Each time the customer uses this “no upgrade” trip template in
the booking path, their upgrade will be declined automatically. To
correct this problem, customers can access the Flights tab of their
online Profile to add/edit/delete their trip templates.

Please understand we require that you are logged in prior to booking
travel for the automatic process to take place. We apologize for any
frustrations this may be causing you.

We hope the above information helps to clarify the booking process in
more detail. Further, we wanted to assure you that Delta is continually
seeking ways to bring about improvements and enhancements to our
services. Your comments being one of our most valued customers will help
us identify and improve the options you value most and will help shape
the changes we develop in the future.

Thank you again for giving us an opportunity to respond to
your concern. We very much appreciate your Platinum Medallion loyalty
to Delta and look forward to the privilege of serving you again soon.

Sincerely,

Alice Holiday
Medallion Desk
www.delta.com