This is minor maintenance release that is released to fix minor issues with saving Security panel settings when WordPress is working in multisite/network mode. Just to make sure, check all the settings again if you switched to multisite mode from normal WordPress installation.
GD Press Tools Pro 4.0 will be dropping support for WordPress 2.8 and WordPress 2.9. Right now, there are a lot of ‘dirty’ parts of plugin due to old versions of WP, and supporting all that has became a real challenge. Also, adding new features with all that is very complicated and cleanup must be done. 3.9 will be branched so that it can be fixed if needed and you can expect at least one or two minor revisions.
More about GD Press Tools Pro: