Yeah, every time you connect to Ubisoft it overwrites whatever is on your hard drive with whatever they had on their servers.
Your saves are only ever sent to Ubisoft during a clean exit of the game. So if you crash out of the game or never exit the game or don't allow the launcher to exit cleanly (power outage or something) then whatever you'd saved from that session never makes it to Ubisoft and gets overwritten when you log back in.
You might be able to mitigate this by always using a new save name, but that'll get unwieldy quickly. Or constantly restart your game to refresh the remote saves. Or best yet, turn off synchronize saves entirely (click the little cog icon while logging in).
__________________
|