The two are different manually updating avast (and you don't say what, program or virus definitions ?), but assuming that it is the program. Then you may well have the latest program version, but the a manual program check would just say you have the latest version.
However, an emergency update allows for program components to be updated without having to release a formal program update.
If it is still running then there is a possibility that something is blocking it. What other security based software do you have installed (firewall, WinPatrol, etc.) ?