I'm not using multisite, although I am using a handful of good plugins which haven't caused issues on the admin side before though.
The "help improve" message always shows, there's only one button (to deny sharing of statistical data), it has a fixed position at coordinates 0, 0 and clicking the button doesn't do anything.
I'm just learning PHP and I may not understand the code well, but could there be something wrong with the following conditional?
if ( !isset( $options['tracking_popup'] ) && !isset( $_GET['allow_tracking'] ) )
I've recently updated to WP 3.4.1 as well.
EDIT: As an alternative temporary fix, I've edited the class-pointer.php, by commenting out the whole content of the enqueue() function. That portion is responsible with displaying the box on the admin panel.