Many agents are still not used to the new "Reserved" E-Cert system, so there can be instances when they don't place one of your E-CR1s into Reserved against the flight number(s) like they are now supposed to.

So far in my experience, this should not effect your upgrade (or the upgrade waitlist if you had been waitlisted) if they forget to do this. They'll just pull it at check-in like they used to if it clears.

It may even have been entered as if you pledged a paper cert, in which case no Reserved hold is made.

So yes...there is inconsistency.