Same issue with achievements but not with club challenges
I installed it last week and i´m going through secuence 2, well i´ve been rewarded with the club challenge for completing secuence 1 but not the achievement
The only achievement unlocked is the first one "hard wake up" (enter again into the animus)
Regards and sorry for my english
EDIT
It seems that next achievement is for complete secuences 1 AND 2
The locked achievement for completing only secuence 1 seems to be from Liberation
I´ll complete secuence 2 to check
Sorry for inconvenience :P