Enqueued Bootstrap Brakes in sub folders

I have a issue which I describe in detail below.

My Main Domain is main.com.

Installing WP on this main domain creates 3 folders in public_html:
-wp-content
-wp-admin
-wp-includes

If you upload a Theme which enqueues Bootstrap to this wp-content folder (> themes) all is good.

Now, I also have a second and third domain (second.com and third.com)

If you install WP for those domains, it automatically creates folders as illustrated below, in public_html:
-public_html
-second (or third, depends which domain)
– wp-content
– wp-includes
– wp-admin

As you see, it creates FIRST a folder with the domain name (second or third) then, it includes WP INSIDE it.

If you now install the EXACT SAME theme in this new WP install, the browser console will throw this error on the page’s frontend:
Error: Bootstrap’s JavaScript requires jQuery version 1.9.1 or higher

I have made MANY tests.

1. A complete different server(!)
2. Local install
3. Re-installed WP on main domain and second.com and third.com MANY times 🙂
4. Tested the exact same theme on all those installs

The issue ONLY happens when the theme is installed in a WP install that actually sits in such a “subfolder”:
public_html
– second (or third.com)
– wp-content.

When the theme is in a install such as:
public_html
– wp-content

NO Error is thrown !

I can assure this is not due to the theme, as the same exact theme works very good on the same exact server, but as soon you have it in such a “sub-folder”, the JQuery call breaks.

The Theme is also used on other servers, and it does not throw this error.
Also locally it does not throw the error.
The ONLY difference is this “nested” folder in public_html

I need to know how I can avoid this, as it is a not nice side-effect having this error in a “public” browser console 🙂

Am I doing something wrong during WordPress install?

Can you advise why this happens and how it should be solved?

Thank you