Eagle ...Keyboard shortcuts dissapearing?

Hey all,
I am a graphic artist and when dealing with After Effects and Photoshop, you grow to love keyboard shortcuts. I am learning the Eagle shortcuts as it is (I feel) the fastest way to get around. I know that some old school Eagle users like to type everything. Some like to hit the little toolbar buttons. I use a Logitech keyboard that has 18 programmable keys on the left side. This can be 3 layers deep of keyboard shortcuts or text macros. Very handy for my line of work, and now, in my dealings with Eagle.

In Eagle, you can assign shortcuts, but for some reason, some shortcuts do not seem to stay. For example, I assigned split to Ctrl+T (as ctrl+S is kinda important and not something I want to remap). This shortcut works great while I am in the program, but once I quit and then go back in to Eagle later, the shortcut is gone and I need to make the shortcut again. This would not be a big deal, except for that I have made a lot of shortcuts and it is getting to be a PITA to re set it each time. Other shortcuts seem to stay without issue. The one common bit here is that when the shortcuts are Alt+F2 - F12 or just straight F2 - F12, they seem to stay. It is when other combos are used that it gets goofy. Do any of you know why these are being erased (for lack of better term) each time Eagle opens.