At least you can play the game. I don't have any connection to the Blood Dragon service so I can't play it properly in the first place. But I've made smiliar experiences like you. I think you have to be sure to have a connection to uplay while you do any achievments. If not, the system might not recognize it.
I did all the achievments in AC: Revelations The Lost Archive but 4 of them didn't get recognized by uplay because it seemed the game had communication problems with uplay while I played it (I did not know that, how should I?). The problem is now, that I can't do the achievments anymore/again because I already did them. But the information is lost somewhere in Ubisofts system. I had a ticket running for over 3 years (!!!) with the support but they talked in circles and after 3 years they deleted the support ticket and opened a new one. The problem has never been solved... I will never be able to get the 4 achievments unlocked and the Ubisoft support says they can't do anything about it. And this bothers me extremely.
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