Not that it's anywhere near guaranteed, but have you got Safari > Preferences > Security > Block pop-up windows checked?
If "Yes", I don't know if there's any way to keep those MacKeeper pop-ups from popping up other than by not visiting the websites at which they pop up, but I do know, not from personal experience, happily, but from any number of past mentions at FTM, that MacKeeper is to be avoided.
I think this will allow you to place folders anywhere on your desktop and have their positions survive a restart: in Finder, hit command-J and select "Sort by: None".
If that works for you as it does for me, newly created folders and other new items will line up along the right edge of your screen from where they can be moved anywhere.
