So every since launch all the way up till last night I have been able to use my arrow keys to navigate the menus. Suddenly they stop working. I don't have a number pad, none of the macro keys or anything are on. I know the keys still work cause in Windows they respond, and if I key them to game commands they work. For some reason though they just suddenly stopped working in game.

Does anybody know of a fix, or had the same issue?

I believe you have encountered the 1.2 (or was it the 1.02) patch, mine got flummoxed like this too. You'll have to go back to using the W & S keys for up-down, and A & D for left-right.
Until someone comes out with a mod to fix the fix.