Problem scenario
A server is hosting a website. On the server, nmap -Pn x.x.x.x is showing port 80 is listening on the server itself. From another server this nmap -Pn x.x.x.x command is showing no ports (or a subset of the ports) are listening. What is the cause of this?
Possible Solution #1
There is a firewall on the webserver that is causing this. See the posting how to check if a firewall is on.
Possible Solution #2
See the posting How Do You Handle a Discrepancy between NMAP Results?
Possible Solution #3
There is an intermediate firewall between the two servers filtering traffic. Use traceroute for clues or ask a security/network person responsible for such a device.