Sub directories work just fine, at least so far for me anyhow.
It looks to me like in the path to your root blog, the “/” got replaced with “base”
Go to Site admin
Click on Blogs.
Click on “Edit” on your main blog.
Next to “Path” in that text box, it should say “/” and I bet it says “base”
That’s my guess.
If I’m wrong, lets look in your wp-config.php file for something similar.