Permalinks Hitting 404 or “Already Installed”

I am having a permalink issue. I have a multi-blog setup (not using Multi-User at this point, though may in the future). Basically, I have a blog at the root, https://www.rooturl.com. Then I have 5 other blogs in subfolders, so https://www.rooturl.com/health, /fitness, /lifestyle, etc. I can activate and use permalinks properly on the subfolder blogs, but when I turn them on for the blog at the root of the domain, it either gives me a 404 page or sends me to the “You have already installed WordPress” page.

When I activate permalinks, my .htaccess file looks right compared to the other .htaccess files. Here is what is in it:

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>

# END WordPress

Anyone encountered such an issue and how did you resolve it? Do I need to add anything else to this .htaccess file? Are the sub-blogs causing issues?

Thanks
Scott