How to stop auto launch at start up

First check that you do not have iTunes listed in All Programs>>Start up. If it is remove it.

Otherwise do you have any other software on you PC that interfaces with iTunes and is configured to load automatically at startup?

I'm having the same problem since updated iTunes. It keeps starting automatically after re-booting Windows and it bogs everything down.

And it's not listed in my 'Start-Programs-Start-up' folder.

What gives?

Try start -> run, and type "msconfig", this will open a little program showing you all the apps loaded at startup. Look for iTunes and uncheck if necessary. Beware, though, that you are messing with your computer's insides, so be extra careful when unchecking stuff that you don't what it's for.
Everything you do here can be undone, though, so you shouldn't wreck your system in any case.
Hope this helps.