Happened to me as well, unlocked all 4 achievements for lvl 20, got the titles, cartel coins, tokens for speeders (even purchased them) and next day the achievements for hylo, aygo and sana were gone (oggurob one is till ok)
Can confirm that i too have problem with imperial agent chapter 1 achievement and "making the connection".
Chapter 1 achievement isnt granted although the patch notes said that it is fixed.
Also have the same problem with the OP in "making the connection" achievement
EDIT: Logging twice to my Sniper seem to fix the problem with the chapter 1 achievement.Only the makeb achievement remains bugged for me