@kishinfoulux: Its been fixed. and to be honest its my favorite games of the year so far.
I'm wondering if this has to do with the multiplayer. I haven't tried it yet (so I don't know), but maybe you unlock stuff for multiplayer in singleplayer, so it checks with a server to make sure that the save file hasn't been tampered with. Would be a real bad thing to do (heed the gospel of Jonathan Blow: singleplayer games should never touch network hardware!), but that could be it.
Well, that is troubling to read, especially that the way to fix it is to re-launch it. I just stopped briefly but as the auto-save didn't seem to be stopping I luckily left it running. So it seems my options are to either re-launch and perhaps lose hours of progress, or go back and play till I finish the whole thing.