I have spent HOURS on this today learning how Apache and Cpanel work, I am a Windows man and used to IIS.
Anyway I also ran several tests with WordPress and noticed that if I install two identical versions but one has the MU enabled it does not work with this plugin.
All I want it to do is secure the logins and admin area. I am using my own public cert and a dedicated IP (I posted previously about shared cert but now I have my own). When I tick the box to secure admin folders it works perfectly on a single site setup. It displays all pages over http but when accessing admin it redirects to https.
When using an MU site though it fails. As soon as you enable https for the admin area it seems to get stuck in sort of loop. It actually redirects to http version of it. If you enter the password incorrect it tells this but if you enter it correct in then just refreshes. I suspect it has something to do with how the URL is formatted for redirects on an MU site maybe different to a normal site. Is this a known issue?