We have JMS set up on our development server and it works fine. I've copied the entire directory and all subdirectories to our production server to run it, using the same directory structure. Currently, both prod and dev are pointing to the same database. It mostly works, but here are the problems that hopefully someone can help with:

1) The dev server has the "installation" directory, which has been patched by JMS. If I put that 'installation' directory on the prod server, Joomla won't let me into the admin back end, probably due to security reasons. So why does it work on dev, but not on prod? The unix permissions and ownership are the same.

2) Because I'm unable to use the 'installation' directory, the Check Patches says "not OK" on all the files that are supposed to be in the 'installation' directory. How do I get it to work with that 'installation' directory?

3) The file /administrator/includes/defines.php has a line in it that reads:
@include_once ( JPATH_ROOT .DS. 'includes'.DS.'defines_multisites.php' );
If I leave that line in there, then I can't get to the admin backend. If I comment that line out, then I can get to admin. Why does it work on dev, but not on prod? What's the difference?

4) I'm editing this post with this additional issue: on the Check Patches screen, it originally listed only "not OK" for the /installation/ directory and files. So I ran the "install" feature, now it says "Not OK" for almost all of the patches. What happened?

Thanks for any help you can offer.

1) If you have decided to share the users, then the domaini and subdomain are probably different between your dev and prod site.
The restore of the backup also restore the "dev" domains for which is filtered the sessions.
This is a possible reason.
That let me supposed the you have shared the users with the master website.
If this is the case, you will have to edit a "config_multisites.php"p file to temporarly remove the MULTISITES_MASTER_COOKIE_DOMAINS that will let you login in the master.

2) The installation directory is restored by JMS Multisites when you install the patches.
So if you click on the "install patches" this should restore the installation directory.
This directory is only required if you expect to create fresh slave site.

3) If you remove the include, this is moreless like if you remove JMS Multisites and probably remove the user sharing setup that I suspect that you have put between your master and slave with another domain. I suspect that you have a domain that is different between the development and the production and that you have decided to share the users with the master. I remember you that we recommend to consider the master website like a repository or a library where you don't put any data. See tutorial video 0.b slide 21-24.

4) If after click "install patches" you get almost all the patches uninstall, this probably mean that you have a permission problem somewhere and that it was not possible to install a patch.
In this case, JMS Multisites restore all the files it has backed the first time and therefore "unpatch" all the files. This is a security procedure to avoid inconistency in the patches. We prefer to have all or none patches installed (with few exception that are not critical).
So check the permission on the files and folder to verify that are owned by the same user.

Thanks again Edwin, you're awesome. FYI for others searching this forum:

1) Yes, my dev and prod domains were different and that's what was causing most of the problems. The config_multisites.php file is in /(root)/multisites/(site name)/ and it needed to be changed to the prod URL.

2) The rest seemed to be a permissions/ownership issue. I recursively changed all Joomla and Site directories to be owned by the same user and permissions 775 (hopefully that's not too liberal of permissions). This allowed the patching to work and to recreate the /installation/ directory.