dolot
1) Why does it block the popup for the second window and not the first?
That is a bit strange, as I would think that it should be blocking both (or neither).
dolot
2) Why does it only do this on my site and not on the jsbin example above?
Not entirely sure on this front either. It sounds like it would be some possible browser-specific settings (e.g. like a popup blocker) or it could be related to the use of localhost. If you have it as an option, you might try explicitly deploying it on some local site to see if the results are still the same.