404 when i try to reach subdomains or phplist

I have a hosting package which uses Cpanel. I have a .htaccess file in my public html folder which points different domains to different paths, e.g.:

RewriteCond %{HTTP_HOST} domainname1.com$ [NC]
RewriteCond %{REQUEST_URI} !^/other/domainname1/.*$
RewriteRule ^(.*)$ /other/domainname1/$1

But, when I setup a subdomain, or installed phplist which result in relevant subfolders in public html folder, it seems to be setup correctly, but when I try to access them at say domainname/phplist/ I get a 404. Same thing with subdomains, e.g. subdomain.domainname.com even though the files and folders are where they should be.
I'm guessing this is something to do with my .htaccess being used in this way to run multiple domains off one hosting account?