Let's see a screenshot of msconfig>Startup and >Services tabs (after Hiding all MS Services) to see what was deselected that might have caused such a problem. But I doubt any of them did. We recommend running a Clean Boot here for best performance, with only the AV and any sync starting with Windows, since most all others are freeloaders intending to spy and not at all needed.

In fact our tutorial for Startup Programs - Change has almost 4 milliion views and I can't remember anyone reporting what you did. So it's likely something else.