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Emptiness 1.13.3 produces two separate sets of page links in the menu to the left of the header image. The first is below "Home" and the second below "Login/Logout" such that it will display:

• Home
• Page1
• Page2
• Feed
• Admin
• Logout
• Page1
• Page2

Prior Reports

The issue is first found reported by jordan on 2011-02-24 at cliffano's blog:

"- if i leave the header left sidebar free of widgets, it defaults to the Home, Feed, etc. links, which i really like — but it includes pages I created twice (in this case, just About)."

To which cliffano replies:

"2. Double up on page links problem is a known issue (other user reported it before) which I could reproduce but still can’t figure out what’s causing it and what’s the proper fix.
The workaround is to create a custom link to a website that is relevant to your blog. On the admin screen, on the left sidebar, there’s a section Appearance -> Menus, add custom link to the default menu, then save the menu. The double up will then disappear."

This issue is also described by cliffano in the FAQ at bitpress.googlecode, last updated 2011-10-11:

"Q: Why is there a page/menu link showing up twice on the header left?

A: Some users reported this error which I can't reproduce consistently. One of them advised that the duplication disappeared after adding a custom link via Appearance -> Menus."

The issue is also reported in comments on the same page on 2011-03-10 by Lance Walters:

"Great theme, thank you. I have having an issue with pages being listed twice in the 'header left' space, and cant find anything in the code as to why. Appreciate any help."

There is no reply from Cliffano.

The issues is also reported at wordpress.org by roxette cassette 464 days ago (~2011-11-03).

And also at wordpress by frustrated1 622 days ago (~2011-05-29).

It is not clear whether cliffano was aware of the wordpress comments.

Fix #1 leaves us with non-backward compatibility.

Need to ensure backward compatibility for the replacement of wp_list_pages() with wp_nav_menu() (See WP First Aid article).