First verify the version of JMS Multisites that you are using.
Fix was delivered in JMS Multisites version 1.2.21.
www.jms2win.com/faq/change-history-v12x?start=20
You have to add the port in the list of domains of your slave site otherwise, it is assumed you are working on the master.
So add in your domain list something like
www.domain.com:80 and domain.com:80
If you are working with https, use port 443.
The XMLRPC protocol adds the port in the URL and therefore must be present in the slave site definition to be recognized as a synonym of the slave site.