Hi Ian,
It's at the same time easier and more complicated than you think

And there's a lot to say about it.
First, what you noticed about the tiny score one gets from a (otherwise perfect) flight is true, this is how it works currently. Without any penalties one gets roughly 20pts per flight hour (in fact it's slightly more for online flights).
Penalties on the other hand are very severe; whatever you do wrong, chances are you'll get a negative score. Personally I gave up and re-flew some flights better that let my score deteriorate dramatically - but this is a matter of personal preferences and priorities.
This being said, you may consider this scoring can be improved, and if you do, you will be right. In fact, you may have noticed that there are discussions in the forum about a new ProPilot scoring system. This will probably happen, but for now we are only discussing the concept, no development has been made in this direction.
So everything should happen according to the "small bonus, large penalty" system I described above. Should, but does not always, and this is unfortunately about a bug we cannot correct yet. After some events (and particularly crashes), a pilot's FAC is incorrectly computed. But things get back to normal after his next uneventful flight.
This is why the scores sometimes look bizarre (and change in a still more bizarre manner). And of course, we apologize for the inconvenience...
Andrei