IME, you must clear & have a seat to show up on the list before check in. There are several instances where I get an email saying I have cleared, but don't have a seat assigned and to do this at the airport. At this point, I'll never show on the list. Then, invariably, I'll go online to select a seat, it will err out when I try, and then when re-loading the reservation, it will tell me I'm assigned to a seat that I couldn't have selected since it was shown as taken when trying to do seat selection. Then everything will be normal again - I can change my seat normally and will show up on the cleared list at that point.