... I'd recommend running winpatrol or startup control panel (by mike lin).
It will tell you what is in your startup. It is almost certainly something running in your startup that is doing this.
Go through each thing in your startup and try to identify what it is. Post on here or search google if you are unsure.
I would've thought the tools you mention would've found it but they're not 100% reliable as new things come out but if something is running and changing things, it needs to be 'executed' and the startup programs is a good place to start.