The Saab Gripen aircraft that is mentioned did crash anyway (in its first flight show over Stockholm 1993 http://en.wikipedia.org/wiki/Accidents_and_incidents_involvi...) in spite of that specially crafted fly-by-wire flight software...
The 1993 crash was due to Pilot Induced Oscillation (PIO). This is a general term for situations when the pilot makes inputs to stabilize an airplane, but the inputs instead end up exacerbating the instability. A simple example of how this could happen is if the control inputs for some reason take effect with a time delay: the airplane pitches up, so the pilot tries to push it down, after a moment the transient passes and the plane pitches down so the pilots pulls up, but the previous input amplifies the downwards movement so the pilot pulls up harder, etc.
Several of the first generation of unstable fly-by-wire airplanes had problems with PIO. Unlike conventional aircrafts, where the rudder positions exactly follow the position of the stick, here the desired rudder position is calculated as the sum of two inputs, one calculated from the stick position, and one calculated by flight control software to dampen instabilities.
Early versions of the software was "rate limited", i.e. at each iteration of the main loop the software calculates the desired rudder position and then moves the rudders towards that position at the fastest rate the rudder actuators allow. However, that leads to problems when there are very large transient stick inputs: because the rudders take some time to move, the largest rudder deflection occurs with some delay after the largest stick input (see figure 6 in [1]).
In the 1993 crash there was a wind gust causing a pitch movement, and both the pilot and the flight control software provided a compensation. The sum of the two signals was big enough to hit the rate-limitation, so the response of the airplane was strange, the pilot gave several more large inputs, and there was PIO.
Incidentally, one of the YF-22 prototypes crashed for basically the same reason, even though they run different software. The solution was to develop some new "phase compensation" methods for designing controllers [1].
[1] http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=558586&...
Basically, the plane would have been better off cutting off input from the pilot and flying on its own.
I just read more about PIO and it's funny, it reminds me of a short story I read a long long time ago, written by Arthur C Clarke, I remember the scene in it where a pilot is remote controlling his big space ship or plane of some kind, while standing on the ground. But because the remote is going through a satellite, there is a feed back delay, say 1 second or so. So when he tries to compensate for a wrong turn, a flavor of PIO is induced and the ship crashes. Think that particular story was written in the 40's, good foresight of Mr. Clarke.