First of all, I had the same issue, and I finished 100.

Assuming you got 100% achievement which means you collected everything including chests (I do not know if chests affect the progression, but I collected all), and finished all main/side missions 100%, and your save file shows 100% sync but you have 99 on your Uplay statistics.

There are 2 things to check.

1. There is a story mission that you don't play automatically, but only by 'replaying'. It is the Connor's view of the mission, of Sequence 8.

Note : You might NOT need to do this, to get 100% story completion. After I did this, my progression was still 99. I got 100 after the next step, so I am not 100% sure whether these 2 both affected the story completion or only the next step.

2. You must find all 9 smugglers camps (3 from the main story, you need to find additional 6. You can simply google the locations). After opening all 9 chests, I got 100 story completion. After this step, there pops up a new mission : Mackandal's Secret Stash in New Orleans (in farm area). However, I got 100 before I start Mackandal's Secret Stash (I finished Mackandal's Secret Stash after I got 100).

Good luck everyone!