Hi bigfishweb,
I have been reading this post page several times over the past few days having had the same symptoms on a website that I am running.
I think I have discovered the issue!
nav-menu.php and a discretely added mal-code half-way through it that almost looked like standard wordpress code in the form of a function called ‘my_correct’. It was chmod-ing the .htaccess file to be writable, editting it and then changing it back to 444.
Looks like MartijnAtWordPress also solved it in this way.
