Q:

Disabling startup items that run despite being unchecked on the "login items" list

I have a number of (background) programs that startup automatically on login even though they have been disabled (unchecked) on the Login Items pane of the Users & Groups System Preferences. Examples include DropBox, ChronoSync Backgrounder, and Boingo.
Q: How can I disable/control these login items that don't respond to the systems preferences settings?
Related sub-questions:

Why do the checkboxes in the login items list not work?
What are all of the places that non-system startup items can be found/controlled?

Current system configuration: MacBook (13in Aluminum, Late 2008), Mac OS X Lion 10.7.3 (11D50), But this problem existed on Snow Leopard before upgrading to Lion.

A:

The checkboxes are not for disabling the application launch, but if checked, the application gets hidden as if you were pressing CMD+H. To disable it, select it in the list and click on the Minus-button beneath that list. By that you remove them. You can't just disable them with OS X tools.
To see a summary of all LaunchAgents and LaunchDaemons you can use a software like Lingon or you can have a look at /Library/LaunchDaemons, /Library/LaunchAgents, /System/Library/LaunchAgents, and /System/Library/LaunchDaemons as well as ~/Library/LaunchDaemons, ~/Library/LaunchAgents, ~/Library/StartupItems, and /Library/StartupItems.

A:

All login items are can be found under System Preferences → Users & Groups → User → Login Items which you have correctly noticed.

If you want to disable a startup item you have to remove it.
The checkboxes are merely for hiding.
Note:
Some applications need their auto-login option to be disabled in their applications' preferences.

