calling wordpress from outside

Hi, I’m calling the wordpress from outside the wordpress directory, let me explain this better:

https://mysite/ <—home of website
https://mysite/blog <—blog (powerd by wordpress)
https://mysite/dir1 <—- another directory
https://mysite/dir2 <—- another directory

My wordpress configurations are:
Wordpress address (URL): https://mysite/blog
Blog address (URL): https://mysite/blog

Everything works fine.
Now in my root directory (https://mysite/index.php) I call wordpress to query my last post title, for that I need to include the blog header require(‘./blog/wp-blog-header.php’) and use the wordpress functions. Till here everything works fine. But when I switch to permalinks the problems get to start, the problems are:
– for normal user everything looks fine (pages display well) but if I check the headers they all come with 404 error (googlebot doesn’t like this)

What I’m doing wrong? Can’t I include the blog header from outside the wordpress directory? Notice, without permalink everything is OK (headers return 200).
If you need more clues to help please ask.

Thanks