Continental.com just added my Delta frequent flyer number (from way back when Continental was in SkyTeam) to my reservation, which I bought while signed in and without changing any options.

I changed the details to my CO number using “Edit Traveler”.

Now, after ticketing, the “Upgrade Reservation” link is asking for 15,000 miles, even though I'm CO elite an on a B fare.

…And when I called the elite desk and they looked up my reservation, the “Upgrade” link that let me upgrade properly finally showed up. So no harm done. Weird, though!

So I checked my profile (Home > My Account > Profile > Saved Travelers > Edit Traveler), and sure enough, the “Frequent Flyer Information” was set to “Delta Air Lines SkyMiles - XXXXXXXXXX”. I tried to change it, and got the message

! Continental.com is unable to update your account at this time. To continue your transaction without updating your account, uncheck the "Save to my account" checkbox.

There was no such checkbox, because I was just editing my account; this wasn't part of a transaction.

I deleted my linked Delta account, and now my default is US Airways (which is worse, because it isn't obviously a bug). (I'll delete all non-CO accounts now.)