In my site, WordPress is installed in a subdirectory named wordpress. In root directory I have a .htaccess with the following rule to convert root url to wordpress. The “/” before wordpress is needed with 4.4.2. That’s a change.
RewriteEngine On
RewriteCond %{HTTP_HOST} ^(www.)?mysite.com$
RewriteRule ^(/)?$ /wordpress [L]
Then in /wordpress subdirectory, I have created a .htaccess file which is the standard WordPress one for 4.4.2. No additional rule is needed and it works fine now. Without this file in /wordpress subdirectory I had many problems with multisite.
I hope this can give some ideas to track your problem.