OK. My first idea was not the right one. But the test helped.
Could you put this debug info:
echo '<!-- dbginfo:';
print_r($query->query);
echo 'suppress_filters: '; print_r($query->get('suppress_filters'));
echo "\nis_home(): "; print_r(is_home());
echo "\nscript_name: "; print_r($_SERVER['SCRIPT_NAME']);
echo "\nindex: "; print_r($GLOBALS['wp_rewrite']->index);
echo '-->';at line 392 just below the line:
function pre_get_posts($query) {I now suspect either your index is not index.php or something wrong with the server variable 'SCRIPT_NAME'.
