Currently i am facing an odd problem if the application is accessed by machine s ip address ex: http://123.342.123.124:<port number>/Folder structure and by machine s name, it is acting differently in both the cases ex: http://<machine name>:<port number>/Folder structure
"Acting differently"? What exactly do you mean by this?
HTTP access to any resource is always done by IP address. When you use a machine name somewhere that name is mapped to an IP address. Try pinging your machine name - see if you get the same IP address you expect.
Which web server are you using? It is possible to map (for example) multiple domain names to a single IP and use this to serve different content for each. You could be seeing a variation on the same theme where the IP and machine name are handled differently.