I've got to say, as an avid GMer of the Adventure Paths, I've had quite a few issues with HeroLab. But as you say chiefweasel, the issues are more because the authors want to get creative with the creatures in the APs, more than Lone Wolf not getting this right.
One possible solution from Lone Wolf though, may be an add on (I'm not sure of the proper name, or indeed if this already exists and I don't know how to use it) that lets you change things freely when you need to. As a non-programer (and I mean with NO experience), I can't change too much in the background or create some of the solutions that you Mr Weasel have done (which I have used, BTW, I am having trouble finding them again, but if you could send me the URL that'd be great).
So a simple "in program" option saying "pretty much do whatever you want with this guy and to hell with the rules cause APs are creativity heavy" would be useful. But as I said, as a new user with NO programing skills, maybe this option already exists and I have missed something.
Anyway, I still enjoy HeroLab and when I get the time to create my own adventures, it is going to save me TONS of time with the monsters.
Cheers