I set applications to NOT start automatically but they do so anyway.

[fterh]

Under System Preferences > Accounts > Login Items, I have unchecked all but one application. For example, Dropbox is unchecked. Yet it runs automatically every time my Macbook Pro boots up. (the icon appears on the top taskbar).

Does the checking/unchecking of Login Items really work?

 

[Jolly Giant]

if you don't want applications to start @ boot up, you need to remove them from the login items list.

 

[simsaladimbamba]

That checkbox is to HIDE applications upon startup:

To remove applications from the LOGIN ITEMS list, click the MINUS icon.