Am using Chrome Version 26.0.1410.43 beta in Ubuntu 12.04.
I use pinned tabs for various Google apps (Gmail, Calendar, Contacts, Drive). I also use bookmarks bar for frequently visited sites. If my browser's focus is on Gmail, and I click on a bookmark, or type something into the Omnibar, then the new destination loads into the pinned tab. I would like for the pinned tab to remain protected, so that these behaviors would open a new tab by default.
The same behavior happens on Chrome in a Windows environment.
I use pinned tabs in Firefox and it behaves correctly (new URLs are launched in new tabs and tab is protected). Because of issues with Firefox and Google Talk Video acceleration I need to use Chrome right now.