If you have disabled show recently used applications then recently used applications will not appear in the menu unless you are using the Windows 10 style option (which is the OS menu).

Pinned shortcuts will still appear, is it possible that is what you are seeing?

After experimenting with this problem I would have to conclude that it is a bug.

The divider on the left side of the Start10 menu (see the image above) divides the left side into two parts. The upper half is for pinned tabs - i.e., Pin to Start menu (Start 10) - and the bottom half is for recently used applications, even when the checkmark is removed from Show recently used applications. There appears to be no way to stop the divider from appearing in the left side of the Start10 menu, and it appears whether you are using the Windows 7 Style menu or the Modern Style menu.

Recently used applications appear in the bottom half of the Start10 menu even when the checkmark is removed from Show recently used applications, but see the next point.

When the check mark is removed from Show recently used applications, only recently used Universal Applications appear in the bottom half of the Start10 menu, and then only when they are invoked from Start10 > All Programs. When Universal Applications are invoked from the Windows 10 menu, they do not appear in the bottom half of the Start10 menu.

I still appreciate Start10 and will continue to use it. Personally, I have no use for Universal Applications, aside from the Settings app, so this problem doesn't affect me much.