Problem Solved! So, whatever was causeing my ISBoxer to not close, keeping my PC from turning off and forceing me to force close it via the task manager, was also causing mapped keys to not save. So I was creating them correctly, but because they were not saveing they were not getting pushed out to inner space. I went ahead and erased all key maps and everything else, re-ran the set up wizard, and now I am able to add key maps and they work in game.

On an odd side note, now only the new mapped keys I create show up in ISBoxer. The ones created during the set up wizerd to /assist me and use 1through+ are not visible under the mapped keys menu, though they are working correctly in game. I guess I wont complain since they are working, but If I need to copy them, edit them, or whatever, it would be impossible...

Thanks to everyone who tried to help me figure this puzzle out!