Multi site sub-directory not found

I have been following the codex instructions to set up a multisite. I am using the latest wordpress version with bootstrap.
I have set up the multi site and the dashboard all looks correct but when I go to view a sub-directory, I get a 404 not found message.
I think the issue is in my htaccess file as when I use the provided code, the main site then gives me a forbidden message but if I edit the RewriteEngine line to off from on then it appears again, or if I remove the content from htaccess completely, then the main site shows but sub-directories are still not found. Any help would be appreciated.
This is a test site so I am working on my local server.