I was actually about to post a similar thing. Playing as Macdeonia (1st game), through to about 650AUC, every family seems to have either around 1000 or less than 50 family prestige. This is despite the fact that the Ptolemy family has had the king in power for the entire game, and has been very fertile, providing at least half of my overall character pool at times. They have stayed at 1000, near enough, the whole time.
I don't know what factors are supposed to affect family prestige, but I've had a few families of little note who produced a few characters with great stats, becoming famous generals etc etc, but their family prestige hasn't risen much or at all.
Also when characters from other nations have been absorbed into my character pool, they seem to have the family prestige they did in their previous country. This would make sense in some situations (eg between Greek states), but I find it hard to imagine the Macedonian aristocracy regarding the Scipio family as having the same prestige as the ruling Ptolemaic dynasty!
I really like the idea behind this system, but as far as I can tell it doesn't seem to be working correctly at the moment. I haven't yetplayed a republic, however; not sure if that makes any difference (given that there are elections).
Edit: It may well be a reload problem - there have certainly been many saves and reloads in my game as well.
Edit the Second: It is a reload problem, have just checked. Upon reload, everything set to either 1000 or 0 in the ledger. Running 1.1.
