Update: Issue ongoing.
Additional information - When I started work on this site I had a SharePoint 2010 site open, in SPD 2010, as well to copy some things and review similar source files. I by no means was using SPD 2010 to edit anything in my SP 2013 site, or vice-versa, but both applications were open at once.
I've taken to saving my source in a separate text file so I can copy/paste if I somehow get an old version instead of the current version. My next step when I get a little more time will be removing and reinstalling SharePoint Designer 2013.
Update: Issue Ongoing - response from MPN mod
They told me to contact MS Support. I'll probably try reinstalling the software before burning one of our tickets for the year.
Update 2: Issue Ongoing
I managed to get around some of this by using NotePad ++ and the drag-and-drop web UI to do the CSS files. Designer seems to be doing OK for the master page editing but seems to crash if I try to check in and publish, then check out and re-open the master page in the same session. Soon I'll re-install this pig.