First, JMS should only be installed in the master website and not in the slave site.
The installation in a slave site is just allowed in case where you would like to propose a service to create website from the front-end of the slave site.
If you have the error reported in the "check patches" menu called from a slave site, this is absolutely normal. You can not convert a slave site into a master website.
Concerning the "mobile joomla" extension, if the patch can not be installed, perhaps this is due to a change (revamp) of the mobile joomla extension.
Please send us a copy of the "mobile joomla" extension in the attachement of an email to review it.
See our contact us menu for the email address.
www.jms2win.com/en/contact-us