The new release doesn't fix this directly, but it does things a lot better. Checkins, the way you're doing them, have been deprecated. Instead, you're supposed to create a post with a checkin object attached. You can read more on the page below:
developers.facebook.com/docs/reference/api/checkin/
As for the multiple popups, changing your checkin method will switch to prompting the user at checkin time, so that there won't be a popup for approval during registration.
As for the "Post on your behalf" popup, with our latest release, we've now included support for "Open Graph Actions". These are events on your site (like readin an article, voting on an place, or reviewing a product) to a users timeline. The permission for that is on the initial/first authorization page and not on a separate window. So, if you switched and moved to Open Graph Actions and moved to the new Checkin recommendations, you'd have only one authorization popup.
Hope that all explains, but if you need more information, just let me know!
Thanks,
Alex
Post on your behalf & Check-ins: Two Separate Permission Pages
