Once you check in, you're under "airport control" and thus why when you call they might not be able to add you.
It may sound odd, but not everyone wants to be auto-upgraded. I know of several times where individuals didn't want to be upgraded. Cases like they are traveling with a group and wish to stay together; I've also seen several politicians and gov't workers decline the upgrades and then there are those rare few where the are using someone else's DM # to get around paying fees and don't want to be upgraded for fear it may shine a light on what they are doing.