The environment:
Joomla 1.5.22, Gantry version 3.1.10, .htaccess file created with Admin Tools Pro v2.0.1. Have tried this with a LAMP setup on Ubuntu as well as on a web hosted account with the same result.
Issue:
Gantry has the ability to apply template settings on a per menu item basis. Using the AT Pro .htaccess maker defaults to create the .htaccess file can prevent Gantry from being able to save the menu specific settings. Clicking the Save or Apply button looks like it's saving, but it never completes and you have to click Close to get out of Gantry.
Workarounds:
After a day of testing and hair pulling (Google and the usual resources were no help on this one) I have found two different ways to "fix" this.
Easy way: Use ssh, ftp/sftp, cpanel file manager or another method to rename the .htaccess file to something else, then make Gantry changes, then rename the file back to .htaccess. Of course, your site is less secure using this method since you're essentially turning off Apache security.
Somewhat easy way: Use the .htaccess maker aspect of AT Pro and set Server Protection - Backend Protection to NO, then click the Save and Create .htaccess button. Make your Gantry changes. Then set Backend Protection back to YES and click Save and Create. Of course, you can just leave Backend Protection set to NO if you're OK with less security.
NOTE: The menu specific change ability of Gantry is the only part I've had trouble with since using the .htaccess maker. Other functions seem to work fine with Backend Protection set to YES.
Also, I have the Gantry zipper and cache plugins disabled permanently, so they should not be causing the problem. It seems to be related to whatever Gantry is trying to do to save settings - my guess is the Backend Protection is essentially denying permissions to a pertinent folder or file.