Keyboard shortucts stopped working

My keyboard shortcuts for desktop icons (ie ctrl + shift + ~ for my internet connnection) have stopped working recently, I think this happened after I started using bosskey and including it in my startup folder, but I am not sure. however when I enter the key combination again and apply it, it works for the time the computer is on, but when it is restarted, the shortcut stops working, even though it appears fine when viewing the shortcut properties. has anyone ever experienced this before? what should I do?

 

Another cause for this is using a tweak program like FreshUI to remove shortcut arrows. It is possible that bosskey is removing the CTRL+ALT+? shortcut function, as it is using it.