Because of the url_alias changes in 3.10 (unless you use urlalias_compat) the pathprefix is like the url_alias, in your case 'My First Site'. I don't use path prefix my self so not sure, but guess the reason why 'My First Site' doesn't have a url_alias is because you previously used pathprefix for it.
So try:
A. set path prefix to 'My First Site'
B. recreate url_alias cache (should be possible by editing the node) C. redo the upgrade but disable pathprefix and recreate the url_alias cache first
In my 3.9.3 installation I cleared the PathPrefix settings so the url is like: http://domain.com/my_first_site/page_1
Now, ezcontentobject_tree table has also value "my_first_site/*" for each row.
After upgrade to 3.10.1 (with urlalias_compat and empty PathPrefix variable) I have incorrect value for all path_identification_string in ezcontentobject_tree table.
Now, I have "root//page_1" value for path_identification_string (there is double "/" - there is no value like before "my_first_site").
--edit:
My mistake. I forgot to change RootNode after changing PathPrefix. When I changed both variables upgrade looks ok :)