Problem solved.
Add the this line:-
$_SERVER['PHP_SELF'] = str_replace('\\', '/', $_SERVER['PHP_SELF']);
Just before:-
require_once(ABSPATH . 'wp-settings.php');
In your wp-config.php.
Or is there anywhere I can update $_SERVER[‘PHP_SELF’] before wordpress calls user_can_access_admin_page()?
Yes, just tried the plugin ‘Google App Engine for WordPress’, the same happened when I access the setting page.
I agree with you that I think the problem is more related to Google App Engine, I tried running your plugin in WAMP, $_SERVER['PHP_SELF'] returns slashes instead of backslashes.
Anyway, I have open another post, as I think it might be more relevant to ask people from Google.
http://wordpress.org/support/topic/unable-to-access-the-settings-page-1?replies=1
Thanks for your help.