I've been singed up ay TopGuest for Virgin America and Hilton Honors. Both seem to work only about half the time. I do these check-ins via Facebook.
A couple of weeks ago I signed up for the new CO/UA check-ins (via e-mails from the airline, not directly thru TopGuest). I set CO/UA up via Foursquare. It has only worked once out of about 6 check ins.
The worst part about my failed CO/UA checkins is that they show up in TopGuest as Priority Club points. I've never signed up in TopGuest for Priority Club (don't even know who that is ... Holiday Inn etc??). So instead of CO/UA emails, I get TopGuest emails asking me for my Priority Club number