Ok, couldn't find a happy medium for WAIT_TIME which wasn't too long for weapons with a fast refire time (shotgun, cannon) against enemies with quick flinch animations, but wasn't also too short in some situations for slow refering weapons (ie, the various sniper rifles). So, I bit the bullet and rolled my own synchronization method.
I'm thinking one of the patches since May has made stray triggers more likely somewhere along the line.

The "fudge time" mentioned in the 22 May 2016 update notes now configurable in the .ini. Default now a longer 0.5 seconds, sniper rapid fire was triggering the second hit animation too early sometimes with 0.2s, seemed related to bluescreen ammo on robot targets.

Some of the classes I extend were updated with the Shen's Last Gift patch, so recompiled against new source code.

Stopped targeting camera popping from the stack (again).

Used a different method to trick miss animations into playing, so Perfect Information breakdowns will show too.

Tweaked to avoid corner case which caused second hit/miss animation to play immediately with the second shot ready/aim animation. Little bit of a fudge, so if you have an odd mod weapon which can go from ready/aim to shot landing on target in less then 0.2secs, then the animation will play late.

HotPatch for freeze condition in certain circumstances.

• Fixed other animation caused by the 15 may update, namely that aliens no longer played their "missed" duck&cover animation for missed first shots, or missed second shots if the first hit.
  
• Seperated out shot comments, with the first shot comment playing out over the readying/aiming animation of the second shot.
  
• Removed the rapidfire "activation" flyover when the second shot fires, now looks quite out of place without the return to overhead.
  
• .ini options in XComCinematicRapidFire.ini added to toggle the above two changes, so people can revert if they wish.