The more recent versions of PCGen also use the most recent version of Java, so if Java was what was causing the problem then it is likely that the problems are fixed.
It is faster than it was back in the pre-E-Tools days. It can stll bog down if you have too many characters open, or a huge number of sources. However it now loads the sources with the character if I recall correctly, so you can start off withthe sources you want for the character and leave out the others til you start on another character.
I have not had it lock up on my machine (A Win XP machine.)
Some of the sources that were removed are now creeping back in, with the notable exception of WotC sources. A number of non-WotC sources were removed as buggy rather than because of IP, and those are creeping in even now. And they have added an experimental newsgroup for PCGen on Yahoo, so if you don't mind taking a risk there are a few others you can look at.
The Auld Grump, PCGen, Dungeon Crafter, Monster, and Word Perfect 10 are what I do almost all my adventure design on.