In your litestep\personal\popup.rc file, look for something similar to this:

My guess is it's been changed from that, to something like this, which would create all the double entries:

If you've removed all the entries from your "all users" area, you can just change that to:

...since you aren't using the "all users" entries. But you'd have to keep an eye on newly installed programs that don't give you a choice, and put their shortcuts there.

Best solution is probably just to make sure it's like the original. :P