Question about launching applications using the Cracklock Manager

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Hi guys, I was wondering if you could help me.
I've downloaded Cracklock, and in the documentation it states that you can
either launch an application from within the Cracklock Manager itself, or
by configuring the date/time options and then running it from the icon in
the start menu.
What I don't understand, however, is that surely if it is ran from the
start menu, it would just run in normal moad, without the changes that
Cracklock makes to it?
Does anyone have any ideas?

Thanks a lot,
Elliott.