Edit: In order to allow players to get warmed up for the release of the DLC, Crytek has announced that there is currently a double XP weekend for Crysis 3.
It's time to be a rising star, suit up and head for Rank 20 at twice the pace!
However, it doesn't happen to every game I've tried, and the symptoms vary.
As to the reason for this problem, my best guess is a problem with directx.
To remedy this problem, I tried installing the version of directx that came on the disc.
This fixed the issue of the save games dissapearing.
I tried downloading and reinstalling the directx runtimes, but that didn't help.
All of my graphics drivers are up to date, and I didn't do any other radical changes to my computer since installing Risen.