First, if you use a Joomla 2.5 version, we recommend that you use the latest JMS version.
See the FAQ for the procedure to get the latest version.
www.jms2win.com/en/faq/faq-joomla-multi-sites#cat-122
Second, PHP Notice are not errors.
This is just a notice that is reported by PHP that are related to PHP compatibilities and sometimes also due to change perform in Joomla version that removed some reference.
They are not errors.
Concerning the "Copy failed", as you can read plenty of times in the forum, this might be due to a problem of permission.
So verify that the files can be updated.