I think I got it now. Let's get this over with.
First of all if you want to mess with your registry be my guest (and wear a hat so that you don't pull out your hair, as nothing worked as expected for me there). But I found an easier way that worked for me.
1) First of all open your real Startup folder.
It should be something like:
Code:C:\Documents and Settings\All Users\Start Menu\Programs\Startup
2) Copy anything from there into the Startup folder you have on your desktop.
3) Then drag the Startup folder you have on your desktop to:
Code:C:\Documents and Settings\All Users\Start Menu\Programs
(or basically where the real Startup folder should go).
4) When prompted to replace the files and folders do so.
Hopefully that will solve it, and your next step is to promise to try to convince me not to duplicate your bugs if something weird happens to you again. ;-)
There aren't any good solutions out there on the SERPS so I'm gonna add the error message in case some internet searcher needs help finding this solution:
Startup is a windows system folder and is required for windows to run properly. It cannot be deleted.
If you can edit your first post and change the Title to "Can't delete Startup folder" it will help others in this predicament find the solution.