On my site, summitsips.com I had the prev/next navigation turned on for both the top and middle locations. I like it that way, but today I had to turn off the TOP and go with Middle only because they didn't match! I know, it sounds crazy, but I think I know why--I just don't know how to fix it.
I added a widget called Featured Tag on the left sidebar. Basically, this is letting me display thumbs of posts in the sidebar. the LAST POST of that widget's list seems to affect the TOP located Prev/Next navigation links on single post pages. Then, when ATA displays the single posts in the center column, the TOP-located Prev/Next navigation links correspond to the widget, not the actual single post on that page. In fact, EVERY single post now has TOP located navigation corresponding to that last thumbnail on the widget. It doesn't affect the Middle (or Bottom) located navigation links though.
I am guessing this has something to do with what is effectively a double "loop", one in my widget corresponding to certain tags I feature there, and the main loop. Both must use some kind of "current post" variable and that is confusing ATA when it builds the Top navigation links. It's getting the "current post" from the last item in my widget. Then, when it actually displays a single post in the center column, it gets that post right, and of course, the Middle (or Bottom) Prev/Next nav links are fine.
If this is unclear, go to summitsips.com and click the last thumbnail on the left sidebar in the widget that has the title "Kentucky Bourbon Trail". This takes you to a post from 2/13. It's this post that seems to be referenced for the Top located Prev/Next navigation links (when I turn them on) for all single post pages. Is there a way to fix this by maybe walling off my widget so that it doesn't rob the theme of what it thinks is the current post? Maybe some surrounding code that puts the current post in a placeholder beforehand, then returns it after the widget is done? Just thinking "out loud". I'd rather not abandon my widget, but I suspect it's confusing ATA with a second "loop" on the page.