There is a pretty well known glitch in Alaska's system where upgrades on pmVX metal clear, but only halfway. The person gets upgraded but not rechecked in. They end up on the "awaiting seats" list and usually have to be checked in again at the gate. Depending on route (sfo-sea) this may be what you are seeing as the problem is more likely to show up on elite heavy routes. That or late check ins that have higher fare class or agents clearing nonrevs first. Really the only way to know is booking full fare Y, checking in right at 24 hours, and seeing if anyone under you gets the upgrade.