I'm not really familiar with custom keyboard shortcuts, as I've never used them. I did find a thread on a forum that said to reboot your computer and the changes should "stick". I have no idea if that works, but it's available here. It's for windows 7 but should apply to later versions of windows as well:
https://answers.microsoft.com/en-us/...a-67898969bb8c
So on the off chance you haven't logged off or rebooted since changing the custom keyboard shortcuts for your shortcuts, give it a try and see how it goes. :)