Why do two Chrome windows launch when I click an external link? I've got the most recent version of Mountain Lion installed, as well as the most recent version of Chrome.

When I've got Chrome set as the default browser, and if I close out all the tabs before I quit Chrome itself, if I click on an external link (e.g., from within an e-mail, Tweetbot, etc.), two Chrome windows launch—one with Google (my set homepage) and one with the target of the link.

Not closing out all the tabs before I quit Chrome does the trick, but what specifically could be causing this?
You've set the homepage to open on startup. Go to settings cmd+, check the On startup option there. You can disable it from there too.