Jax's counterstrike still doesnt block empowered autos recently i got flash q'ed by a nasus when i had counterstrike going
it blocks ONLY Auto attacks, the actual q damage goes through, but the AA damage is blocked, at least that is the consensus i have found.
ironically 
stun applies damage as well...
"Historically, the way empowered basic attacks would affect their target if they'd fail to hit (due to Teemo's Blinding Dart, Pantheon's Aegis of Zeonia, or Jax's Counterstrike) has been pretty inconsistent. In some cases they'd do nothing, in others they'd apply crowd control (but no damage) and in a few they'd just ignore the status altogether. We've retooled these to more consistently meet expectations: if one of the following empowered basic attack misses its target, it won't deal any damage or apply any other effects. In cases where this is tied to a buff, that buff will be consumed as well."
That means the Q should apply NO damage and should go onto cooldown. This IS a bug.
Actually this is a bug yeah riot already say that they know that many empowered attack didnt get fix but they would all get fixed in the next patch
So dont worry in the next patch this would be fixed and jax would be able to win some lanes again
BTW its already block leona stun-Q-damage and renekton W-Stun-damage and xin zhao Q-damage-knock up and blitz E-damage-Knock up and TF w-damage-effect
So wait till the next patch where all of them would get fixed
The following abilities will be consumed and have no effect if they would miss: Blitzcrank E - Power Fist Darius W - Crippling Strike Ekko Passive - Z-Drive Resonance Garen Q - Decisive Strike Jayce R - Transform: Mercury Hammer Jax W - Empower Kassadin W - Nether Blade Leona Q - Shield of Daybreak Master Yi Passive - Double Strike Nasus Q - Siphoning Strike Nautilus Passive - Staggering Blow Rengar Q - Savagery Renekton W - Ruthless Predator Riven Passive - Runic Blade Sejuani W - Flail of the Northern Winds Shyvana Q - Twin Bite Skarner E - Fracture Sona Passive - Power Chord Talon Q - Noxian Diplomacy Trundle Q - Chomp Twisted Fate W - Pick A Card Udyr E - Bear Stance Vayne Q - Tumble Viktor Q - Siphon Power Wukong Q - Crushing Blow Xin Zhao Q - Three Talon Strike Ziggs Passive - Short Fuse
This is the list
