I start the game up and for the most part it doesn't happen. But every once in a while I get a message from steam saying something like my saves aren't compatible. It then gives me the option to download to steam or upload it to something else. I click the one that says newer and then I go into the game where I find that I didn't lose all my progress, but I end up losing 2 or 3 of my saves which puts me back by and hour or so.

Sorry if this is pretty vague, I can't quite remember what it said exactly. But it will happen again and then I'll be sure to post what it says.

You can disable cloud globally or for individual games if you have issues with it.