Simulated keystrokes that are intended to trigger hot keys in the system or other applications do not work in Mojave unless they are letters (optionally with modifiers). Simulated arrow keys or function keys do not trigger hot keys due to bugs in Mojave.
This may be fixed in a future version of Mojave, or I may find a workaround in the future. In the mean time you may be able to adjust your hot keys to to use letters instead of arrows or function keys, and then they can be simulated from Keyboard Maestro.
Unfortunately, the system says that Keyboard Maestro has accessibility permissions, but due to a bug in the Mojave upgrade system, Keyboard Maestro does not actually have accessibility permissions after the upgrade, even though the checkboxes are checked, and even though the system tells Keyboard Maestro that it does.
You need to toggle the accessibility permissions (System Preferences, Security & Privacy, Privacy, Accessibility) for Keyboard Maestro and Keyboard Maestro Engine off and then on again (or, I believe, make any change to the accessibility settings will do the trick, but certainly toggling the ones for Keyboard Maestro resolves the issue).