No, the key thing here is that I only have them in either my personal startup folder (and they don't run period), or I move them to the All Users folder, and they run twice. They have never been in both places at once.
The way I know they are only in once place is by right clicking my Startup folder, doing open, then going back and right clicking Open All Users.
Now, this might make a difference, I did at one time accidently delete my personal startup folder, but as far as I know, there is nothing special about it beyond the name and location.