Permalinks and sub folders in url

Hi yea,
I am using the permalinks and all works fine, but....

When I set my permalink i do so as

Permalink
ru/index.php

Custom Source Url
/index.php?loc=1

I see my page https:///www.mysite.com/ru/index.php loads but it doesn't load the css or js file thus it is just a content page. 

===================//

when I set my permalink to 

Permalink
ru

Custom Source Url
/index.php?loc=1

the page https:///www.mysite.com/ru shows up just fine. but if i put https:///www.mysite.com/ru/ the page shows without the css or js. 

I have checked my server path

I would be grateful for any input.

Cheers

Kenny