So far, this only happens during ground missions. It can happen during a Foundry Mission, Episode, Exploration, or anything else; but only on the ground, and never when flying my ship.
Somewhere during the Mission, all my numbers are locked out. I can't use my weapons, Devices, or other abilities with number keybinds, whether pure numbers or with Ctrl.
Note that I'm on a netbook; there is no number pad. I use the number row along the top. I do have a NumLock key, which turns part of the right hand of the letters area into a number pad, but I'm not accidentally activating that (and when I do activate it on purpose, it still doesn't work).
It also doesn't work to use my trackball to click on the controls on the screen. I can click on them, but they still won't work.
This doesn't happen every time; only every once in a while -- like about ten percent of the time. It rarely starts out this way, but usually kicks in about halfway through. And if I go to space and then return to another ground mission, the numbers are working again.
(If I'm the only one experiencing this, then it's probably just that netbook, which is due for replacement in the next couple of weeks, so don't worry about it.)
Same thing here. Experienced it for the first time, after I patched today and began Second Wave. Making Escaping Evnoys VERY difficult as I need to use my mouse to target and fire. Other keys work fine. Restarting the game and re-logging don't fix it either...