Ok, so I just stumbled on to quite a big change in Keynote 6.1, which I recently moved to after upgrading to 10.9.
Apple now by default forces you to save Keynote presentation (and evidently all iWork documents) as packages. This is nothing new on Mac, per se (we use it within Accordance as well), but what I noticed tonight is that Dropbox does not recognize these new packages as flat files, but folders, and very importantly does not retain version history of folders, only individual files.
In Keynote '09 (v. 5.x) you had a preference whether you wanted it to save presentations as packages (screen shot below). This preference is gone in Keynote 6.1!
Screen Shot 2014-03-31 at 8.00.15 PM.png 126.65KB 2 downloads
I did a save as (which you can still access with opt) on a presentation and renamed it only to find out that Keynote saved over the previous version and dropbox didn't keep an older version of it. Thankfully I had a TimeMachine backup. Just thought others might find this helpful in case you rely on Dropbox for version history.