I had this problem quite often too and it was making me crazy. The solution I found is really non-intuitive. I had opened my keynote file using the finder and I still had the file selected by the finder as I was working on it. If you change what is in your finder window to be something else other than the keynote presentation (I usually go to a completely different folder) it seems to stop it.
I verified this by looking at what was happening in the Console. With the file selected and me working on keynote I was getting tons of errors. Once it wasn't selected the errors disappeared. Good luck!
Sorry that I'm spamming this on several related questions but this does work and the problem was making me crazy!
An entry in https://discussions.apple.com/thread/5497463?start=0&tstart=0 that talks about Dropbox triggered me: my .key file is situated on a Synology Cloudstation. After pausing the Cloudstation syncing, I don't experience the problem.
Running Keynote 6.1 on Maverics 10.9.1.
I have been struggling with this for a year. If you click "save anyway" Keynote loses a good amount of your media; if you click "revert" at least you can get your file intact from a few changes back.
I noticed that I ended up often with a file bearing the same name as my keynote folder with some of the media in it; I could tell that it was a copy of the innards of the Keybnote package when you open a presentation from the finder. I was able tio restore one damaged keynote presentation (it went form a 50Mb original down ro 11) by copying the media from a backed up version.
But today, my finder window was open, and I could actually see this folder being generated, and then it would disappear. My hunch was, and from what I've always noticed, is the keynote is doing periodic autosaving.
There is no oreference to change this, but I have found the command line to turn this off. Just open the Terminal, enter:
defaults write com.apple.iWork.Keynote ApplePersistence -bool no
and press return.
Boom! No more autosaving, and no more error messages, and no more corrupted keynote files. Here is the post where I found the answer