Just FYI - the link I provided in my original post for the FAQ.. I just checked it today, and they updated it as of September:
Modified on: Sat, 6 Sep, 2014 at 12:53 pm
There is a new option we've added to Wordfence to fix this specific issue. If you're having the trouble described above, scroll to the bottom of your Wordfence options page. Check the box next to "Disable config caching". Save your options. You should now be able to save any other option changes, change your API key and this should also fix any "cron key errors" you're having.
So it seems I was not the only one having this problem... I checked that box, and like magic it started saving my changes. Thank goodness, I haven't really had time to search for an alternative to WordFence.