I'd call Delta and ask the agent to work through check-in with you so they can see any error. I had a similar issue a couple of weeks ago due a ticketing issue after applying GUC. Delta said everything was fine until I got the agent to try and check me in, at which point she saw the problem, contacted the KL/AF supprt desk and their agent fixed it.

I flew the 6am MAN-AMS flight yesterday and there was a long queue at 3AM which is when the check-in staff start work. Security at MAN can also be a pain - they seem to run the scanners on super-sensitivity and a large proprotion of bags seems to get sent to secondary screening. I've taken to taking out pretty much everything that could possibly trigger the scanner and dropping it into the tray as a loose item.