Kremmen,
I had to go through several conversations with both AS and CO on this to get it fixed. I was told by CO to call AS myself and to find out what the original fare code was before the upgrade. The AS agent will have to ask a supervisor to find it for you. Then you will have to call back to CO (and probably write them also) and give them the original fare code and then cross your fingers and start praying. The CO Mileage Plus Agent told me that their training manuals state that 'A' & 'W' fares on AS do not receive CO miles. I really had to explain to them that 'A' fares are upgrades.
Good luck with your new mission on getting the miles.