It seems like I'm not the only person having these problems, but I thought it was worthwhile to share my experience to see how many others are having the same issues.
I have several customized quick keys set up in InDesignCC, along with the default keyset. Some appear to work more or less correctly, some--a good example is "Links/Edit Original", which I attempt to use fairly regularly--don't work at all. Even a default quick key like Save As (cmd + shift + S) doesn't work. All that happens when I try to save as, is the word InDesign in the menu bar flashes every time I hit the key combination. Weirder still, if I put my cursor in the menu, and show the file drop down, and THEN try the quick key, it works just fine. I haven't made any system changes or updates, and this is something that's only a problem with InDesignCC (though I have had some similar issues with IllustratorCC), all my CS6 applications work fine. I've even looked through my keyset to make sure that there weren't any conflicts that I was missing, and there weren't. Does anyone have any ideas on how to fix this, or is anyone else dealing with it themselves?