In 6.09.00, after loading the sources (PF or 3.5), pcgen completely stops working. I can't select anything or click on anything; it's like having a screenshot of the main page.
I think I know the issue, after loading sources the gaming license notification popped up and maybe it drew behind the PCGen window? PCGen waits for your confirmation when it displays the license before proceeding so it would seem stuck. There is an option to disable license display in preferences and the license dialog itself.
Can you retry again after disabling the license popup? For the preferences route it is Tools >Preferences > Sources tab > Uncheck Display Open game license on source load. Hope that solves this.
Been long enough, closing as cannot reproduce.