I just went and logged into the test site to see if the update was there approx an hour after disabling the security plugin and the GP Premium plugin is now asking to upgrade to v1.1 so it appears to takes some time to pull down the update. It appears to take longer than I first thought.
I will do some more testing to make sure it is the .htaccess blocking the update. Just wanted to let you know before you waste any more time on this issue. Will update thread as soon as I have confirmation.