Custom Key command prefs not sticking

I am big on making my own key commands for the tools I use more frequently. Since the last update, it is almost as if they just arent sticking. I will edit them and make sure that I have them correct the way I want them in the edit keyboard shortcuts window, but then when I go to use them they use the normal base key command. 

For example, I use ⌘E for Expand. I changed the View as GPU/CPU command to ⌘F6. But when I leave keyboard shortcut screen and try to use my new command for Expand, it still does View as GPU. And when I go to the dropdown for View GPU it still shows ⌘E next to it. I have my keyboard shortcut preferences selected so I don't get why it's not working.