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