Autorun, why doesn't it show changes made in services.msc?

Hi all.
I’m a bit confused by the way the autorun analyzer works…
It’s a tool to disable unnesessary autoruns, right?
When I first ran AA, everything was checked. Even the things I previously disabled using either other software, or the services.msc utility.
eg. I disabled the “alerter” service using services.msc, yet it is checked on in the autorun analyzer?
I’m confused… ???

On what OS are you?