First JMS should not be installed in each website.
Only the master website should have the JMS installed.
If you try to install the patches from a slave site, the "install" button is disabled.
If you have the "slave" that is display when you go in what you expect to be your master then I repeat, this is because the slave site is in fact your master.
The master website is any domain or subdomains that is not defined in the list of slave site. Therefore if the URL that you provide to be the master display the slave site then this mean that in fact this is your slave that is the master.
If you want that we have a look in your environment, this is still possible with our billable support that you can order at
www.jms2win.com/en/joomla-multisite?page...35&category_id=1
Verify the "configuration.php" file of what you think is your master (here probably the slave).
You can also check the different structure on the disk to try identifying for sure where your master website is located and which is its "configuration.php" file.