Guys, the thing that causes this is clicking the single player button before the version finishes calculating the checksum. There are two indicators on the main game screen that show this. First, in the bottom left hand corner next to options (or credits, or whatever button is in the bottom left-hand corner of the menu), there's a small black box that normally shows the checksum of whatever version you are playing. When the calculation hasn't finished yet, it'll instead say "calculating version..." or something like that. Second, and more obviously, the multiplayer button (right next to the single player button for those who don't know for some reason), will be grayed out until the version finishes calculating. If you hover over the button, it'll say "Please wait for the version to finish calculating before playing multiplayer" (or something like that). The reason why this is important is that the game verifies a save is ironman by making sure the checksum hasn't been altered; if the checksum hasn't been properly calculated yet, the game will interpret it as having been altered, thus any ironman game you load in this state will be de-ironmanned.
So basically, the problem is that you lot are a whole bunch of impatient buggers. So if you find yourself having the irresistible urge to click the button as soon as it pops up cause you left off in a great spot and that achievo is soooo close AND ERMAHGERD IMMA REMOVE BAG- slow down, calm yourself, take a few deep breaths, and I don't know, bob your head to the main screen music? Pick your nose? Frankly, I don't care, just wait for the version to calculate.
Or, you know, Paradox could make the main screen wait to pop up until after the checksum has been calculated. But that takes effort!