On my test server the redirect rule for the www of the main domain gets added too correctly, so there is no problem with ISPConfig. Maybe you edited something in your setup that causes this.
main domain: test.int with auto www enabled produce sthe rewrite rules:
RewriteCond %{HTTP_HOST} ^test.int [NC]
RewriteRule ^/(.*)$ http://test.com$1 [R]
RewriteCond %{HTTP_HOST} ^
www.test.int [NC]
RewriteRule ^/(.*)$ http://test.com$1 [R]