Unlike the previous version, PCGen 6 does not allow creating a new deity from the normal UI. Right click on "none" for deity in the domains tab does not bring up a context menu.
Windows 7 64bit, German
Yes this is expected as a result of removing the list editors. For the moment any deities will have to be created as a homebrew set. See http://www.pcgen-test.org/autobuilds/pcgen-docs/listfilepages/lstfileclass/lfc_lesson00_homebrew.html
Will be dealt with in the linked project.