Oh my how I beat myself in the head till I discovered this is a repeatable issue in the latest 'fix' release
Mac on both 10.11 and 10.12
FMPA versions from 14.0.3 to 15.0.2
Create a simple script
custom dialog with the body Get ( ActiveModifierKeys)
In all version EXCEPT 15.0.2 you will see 2 in the dialog when the short key is pressed, in the newest version you see 0. that's right 0, so alter navigation I am just building will not work to redirect to another layout based on a modifier key.
Created file and taken it round all the machines in the office, and it is ONLY problem in 15.0.2, but that means this update can not be installed, leaving all the other fixed thing broken
Try with this file..