I want to add a quick note, though I'd still like to hear what people have to say:
I tried running in safe mode, disabling all Add-Ons, and saving in Dropbox, Google Drive and SkyDrive... however, none of those was related. It was really the Ink Tools. Here's why:
I found that when using Ink Tools, sometimes there are little tiny ink dots left behind... you can only see them if you drag-select all of your ink annotations. I don't know if this happens when the file crashes when you Undo too fast while inking.
If you move these little ink dots, and then try to save, you get the unstable error message.
If you delete them, you won't get the unstable error message.
I also found that if you GROUP them with another valid ink line, they don't cause a problem.
However, I have yet to find a way to detect them other than going through, slide by slide, selecting all ink and moving it slightly to the left or right, then saving. I went through all 250 (!) slides of my presentation to do this. It was painful.
Please, if someone finds out what causes these little corrupt ink dots, I'd be eternally grateful! I can provide an example powerpoint file that has the problem if you want to check it out.