One of the problems is related to family trees, you're right (specifically it's that the heirs for some factions aren't linked into the proper family tree in the released version, and then the family ends up with two characters with the same name and internal ID at times and that confuses the program to death).
We are (slowly but surely) working on a version with more fixes, and a few new unit types, and campaign win conditions, hopefully to be released sometime in early 2013 (work is slower as I'm now at university).
Disabling autosave sometimes but not always seems to help.