What is the difference between Fly-By and Short-Turn? By all definitions that my team and I have found, fly-by and short-turn (with respect to military unmanned air vehicle waypoint based flight) mean the same thing.  Briefly, this allows the pilot to fly within a capture distance of the waypoint but is not required to fly directly over or through it.  In other words, the pilot can start turning before the waypoint is reached.

Current Definition:
A short turn will be performed at the turn location.  A short turn indicates that the vehicle may begin its turn prior to reaching the waypoint and fly-by it instead of through or over it.

Is there any nuanced difference between these two states so that I might further clarify this in my definition?
The context of your question is a bit unclear, but assuming that you're asking about navigation waypoints in the US then you're probably referring to these terms as defined in the FAA's Pilot/Controller Glossary:


  FLY-BY WAYPOINT- A fly-by waypoint requires the use of turn
  anticipation to avoid overshoot of the next flight segment.
  
  FLY-OVER WAYPOINT- A fly-over waypoint precludes any turn until the
  waypoint is overflown and is followed by an intercept maneuver of the
  next flight segment.


As per the comments, I have never heard of a "short turn" waypoint and it isn't in the P/CG.