If you drag a shortcut to the quick launch bar in liberkey (holding down ctrl so you make a copy and not move it), you will get two entries in the recent/most used menues for this application. One entry from the "regular" liberkey shortcut, and another entry from the copy that resides in the quick launch section (after you have launched it at least once from each location). Creating a custom menu and launching it from there creates yet another entry in the recent/most used menues.

I know you can edit the shortcuts to prevent the copies you have made in the other menues (quick launch and custom menues) from appearing in recent/most used at all, but this kind of defeats the purpose of the recent menu, and even more the "most used" menu.
Both of these should really treat all shortcuts leading to the same application as a single entry in the menu.