WordPress version: 3.5-beta1-22204 (though the described behavior has existed for a couple of days)
WordPress SEO version: 126.96.36.199 (which is also the latest development version)
I did this: Using Chrome and Firefox, Twenty-Twelve theme, and no plugins other than WordPress SEO active, I went to the post edit window and clicked the Beta Upload button and the Upload/Insert link. In neither case did the modal window appear.
Deactivating WordPress SEO restored proper operation; the modal windows appears when the button and link were clicked. Activating all my other plugins did not change the behavior.
I expected the plugin to do this: See above
Instead it did this: See above
Yes, I know I am operating on a very early version of WordPress. Just giving an early head's up.