I was planning to post an update about this, but I can’t make it any simpler or clearer than Misha has put it. The forum on issues with the new Reader is now 8 pages long (http://en.forums.wordpress.com/topic/reader-changed/page/8?replies=147).
Tired of having to open two different pages to get to blogs that you want to read in the new WordPress reader? Last night I happened upon a way to go directly to the blog without going through the pop-up first.
So far this seems to be working with all the blogs that I’ve tried.