Perhaps the programs are adding themselves to the startup Run keys, or they're running as Services?

See also:

Error message when you start a Windows Vista-based computer: "Windows has blocked some startup programs":
http://support.microsoft.com/kb/930367

I have used System Configuration, Startup to NOT start some programs
including:
OmniPage Pro
iTunes
QuickTime

How do I prevent the message that pops up several times when I start/restart
Windows Vista? Even once would be enough....

    You shouldn't use msconfig to block your startup programs. The best way
to block a program from starting at bootup is to go to the program's options
and see if there is a way to configure it to not run at startup. You will
sometimes have this option at the time of installation. If you have no
option within the program itself you can use Windows Defender to stop the
programs from running at startup.
    Open Windows Defender and click on Tools. Click on Software Explorer,
select "Startup Programs" next to "Category" and then click on the button at
the bottom that says "Show for all users". Choose the program you do not
wish to run at startup from the left pane and then click on the "Disable"
button on the lower right. Do this for each program you wish to disable from
startup. You can still use all the programs you have disabled. You are only
disabling it from running at startup. To run the program when you desire you
can go to Start, All Programs and select it from the list.

C.B.

The best way to disable a startup item on the computer is using the
Windows Defender. This holds the control of the Startup items.

Click Start  , Control Panel , Security , and then Windows Defender .
At the top of the window, click Tools .
Click Software Explorer .
The Software Explorer window opens.
In the Category field, select Startup Programs .
In the left panel, select the software programs you do not want to
automatically start when your computer starts up.
Do not select any items you are not sure about.
Click the Disable button on the lower right