Some shortcut keys randomly not working

I'm having a weird issue where at random times, some keyboard shortcuts will refuse to work. This happens consistently on both the native MacBook Pro keyboard as well as on an external Apple keyboard so it's not an issue with the physical keyboard. Cmd+C, Cmd+V, Cmd+A, Cmd+~ will stop working, but many other shortcuts involving the Cmd key (Cmd+tab, Cmd+W, Cmd+Q, screen capture shortcuts, etc) will work perfectly fine. If I restart my laptop, it'll be fine for a random amount of time, and then it'll start happening again, so it's not a shortcut mapping issue either.

I'm using a late-2013 MacBook Pro w/ Retina running OSX 10.9.5.

Thanks in advance!