I have a site with a horizontal main navigation that is using the auto-nav block to display only the top level pages. My site map looks something like this:

Home
>Top Page 1
>>Second Level Page 1
>>>Third Level Page 1
>>>Third Level Page 2
>>Second Level Page 2
>>>Third Level Page 3
>>>Third Level Page 4
>Top Page 2
>>Second Level Page 2
>>>Third Level Page 5
>>>Third Level Page 6

The main navigation works fine. But on sub pages I have a sidebar also using the auto-nav block that displays all the subpages (both second & third level) to the current top level page or parent page. So on Top Page 1, I have an auto nav with "display second level pages" and "display all subpages". I add the block and the list looks good:

>>Second Level Page 1
>>>Third Level Page 1
>>>Third Level Page 2
>>Second Level Page 2
>>>Third Level Page 3
>>>Third Level Page 4

But whenever I exit edit mode the list changes to only include 1 of the 2 second level pages and children:

>>Second Level Page 1
>>>Third Level Page 1
>>>Third Level Page 2


Using firebug I can see that when added in edit mode the list looks like this:
<ul>
<li>Second Level Page
<ul>
<li>Third Level Page</li>
</ul>
</li>
<li>Second Level Page
<ul>
<li>Third Level Page</li>
</ul>
</li>

Using Firebug I can see that the second <li> that holds the second Second Level page is not even there when not in edit mode.
Also if I switch back into edit mode it does not revert back as if I had just added it.
It's very strange because I have successfully done this same thing on another site. What's going on?