This issue is another reason I get annoyed when upgrades don't clear at the expected window. I know I have to babysit my reservation as long as upgrades haven't cleared because I fully expect to have to change my seat assignments as soon as an upgrade does clear. I know, a first world problem, but I truly do care about seat assignments. This system forces me to spend time and energy to get what I want--not very customer friendly.
Oh, and if the email notification system worked perfectly that would help some. I don't believe it does, though, so I can't rely on it.