You did not answer my first question. So I must guess it is intentional and you do want it for a single program. Since you are targeting a single program, what is this program ?
For a single program manually entering it in a context menu is the straightforward way. Now you seem to claim that you have a script that is working for folders only, can you show this script and a print screen of the registry section. I do not understand how a SetOnTop is working for folders only (that does not make much sense to me).
ps. I need to extract from you every piece of information, it would be nice if you could provide a more complete description.