This was happening to me as well – though I was not using a .htaccess file.
I was attempting to build a mod_rewrite class in php (404 handler) for IIS6. Yes I know there are some snippets out there, but I wanted one that could handle the same rules xml that IIS7 used, and be very generic.
I found that if I included the WordPress index.php file from within a function in my modRewrite class, it failed with this error – but when I included it in a global scope (outside of the class) it worked just fine.
Just thought I’d share my findings.
