I have the same exact problem. I got the game early for Christmas and I played yesterday for 8 hours and manually saved the game about 10-12 times. I started the game and selected continue and I am now so far behind where I was yesterday. This is total BS for a PC game that can't save correctly. I mean, who the hell is behind the QA testing on this should have know by now that this is an issue. I'm totally pissed. A full day of progress is all gone.
I'd think someone at Ubisoft would rush a hot fix for this before people start posting this problem on retail sites like Amazon.com and all the other game sites like Steam, etc. You can count me in on that action if this issue isn't corrected very fast...and by the way Ubisoft...Merry Christmas to you too!!!