Perhaps, if your printer has the feature, the print head needs aligned. This is a feature our HP printer has and occurs automatically when the ink cartridges are replaced. It's also something that can be done even if the cartridges haven't been changed.
I don't know what occurs during alignment but a test page is printed then placed on the scanning bed. The printer then goes through a series of checks, the print head seems to be moving during this time, which I imagine the printer is comparing what's on the test page with the paper in the printer to make sure the head prints according to programmed parameters and is positioned correctly to do so.
As to not being able to scan something, that wouldn't have anything to do with the print head, at least it doesn't on our printer. I would imagine the major cause of this problem would be troubles with the printer drivers. And getting the scanned item to the HD dependent on how the printer connects to the computer.
If something gets your goat, it just proves you have a goat to get.