Yesterday while playing SS for many hours my hotkeys suddenly stopped working. Item, Radar, and Squad windows would minimize but then was unable to bring them back up unless I manually clicked on a button at the bottom. I logged off and the hotkeys all worked again. But again a few hours later, same thing happened.

I've had this happen too.

All the time after some time, but I can never get ahold of Jey on IRC to tell him >.<

Same here, and other teammates have reported it as well. I just hadn't gotten around to reporting it myself since it is rather intermittent and I initially assumed it was something on my end (using wine).

Yeah, it happens for i, o and p for me. u worked.

Also, after some time, your galaxy map will get messed up as well.

Indeed, and it's important to reiterate that these keys work to close the windows, but not open them.

My custom keys like ~ for inventory wont work aswell, well precisely it wont open inventory.

Same issue here, all keys which open up a new dialog box seem to stop opening up dialog boxes. However movement, firing and other keys which do not open up a new dialog box continue to work.

confirmed I had this with the inventory the other day, would close it but not open it

The bug is triggered by clicking "Ok" in the options window. For now, avoid that by closing the window with "O" but there is a fix waiting to be patched in.