When you re-install an extension in a slave site (component, module, plugin), this physically re-install all the things (DB AND php files).
This is the reason why JMS checks that you are trying to re-install the same version than the master one.
In this case, you have configured your website to use the FTP layer (JFTP error message).
This probably means that the user has not the permission to rewrite the extension.
To avoid re-installation of the PHP code we have created the JMS tools that only fill the DB and does not recopy the PHP files as they are already present.
This tools need that we review manually each extension to discover the DB tables they are using and what they fill in the DB joomla.
Unfortunatelly, the JoomSEO plugin is not yet defined in JMS tools.
Send us in attachement of an email this extension and we will have a review to see if we can add it in a next release of the JMS patches definition.
See our contact us for the email
www.jms2win.com/contact
So for the moment, you probably have to change the permission of the joomseo files or perhaps change the FTP user / password to be comptaible with current joomseo permissions