We have Jetpack 1.2.2 installed now on our multisite network. I connected all sites on the network to WordPress.com using the same account.
I added the subscription widget to the main site in our network. (For testing, I also added two other sites.)
When I subscribed to the main site (blogs.princeton.edu). The confirmation email came back from "My Site." The subject said "Posts on My Site - please confirm." And the header text in the email said "Subscribe to My Site!"
When I tried the same from other sites in the same network, the site's title was correctly inserted into the three places in the email. I also tried this with the main site on our -qa network, and the site title was fine.
Is it possible that there was a problem with the initial Jetpack activation on that site that caused the site title to not be picked up, and it was replaced with "My Site"?