Taking a logical guess…
Looking at your thread history it looks like you have a Network/Multisite site. We changed the htaccess writing code (root htaccess file) for Network/Multisite and have noticed that in some isolated cases depending on the site type and folder structure the correct htaccess code is not being created. Since we are now using the same code that WP uses (yes we “borrowed” it) to create the Network/Multisite root .htaccess code we know the code is good of course (see Note), but we have a Network/Multisite test site that has an unusual/unorthodox setup and the root .htaccess code that is created by AutoMagic does not work / is incorrect for that particular setup/installation.
That test site is a Network/Multisite subdirectory site installed under another folder (website) and is a subdomain site. The URL looks like this: subdomain.example.com. The folder structure looks like this: /example.com/subdomain/. So we are not surprised that the correct root .htaccess code is not being generated by BPS AutoMagic because this is frankly a very unorthodox/nutty setup just for testing purposes.
In any case, what we have decided to do is this: Create another BPS Custom Code text box just for cases like this where the Network/Multisite site is not installed in an “out of the box” default way/installation. The additional Network/Multisite Custom Code text box will allow someone to save the correct rewrite code for their particular Network/Multisite setup in cases where they have an unusual setup. This is of course only necessary for “unusual” Network/Multisite setups/installations. All other “out of the box” Network/Multisite setups/installations AutoMagic writing is working fine and writing the correct root .htaccess code when clicking the AutoMagic buttons.
Note: Another possibility is that we did make one change/adjustment to the WP Network/Multisite root htaccess file writing code and the change we made may not work correctly in all cases. We are looking into that if that is the issue/problem we will fix that. In any case, the additional Network/Multisite Custom Code text box will be created since it is a good idea to have this just in case.