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You are putting a lot of effort into making your question as hard to read as possible :/
The heart of the matter is this:
Now I have added a simple code System.out.println("check point one"); with other SOP. After addition of a small code I run the server, and when I check the output I donot get my newly added SOP message. The out put that I get is of previous code.That must mean the updated .class file that Eclipse created (assuming build automatically is switched on) is not deployed to the tomcat instance you are using. You need to figure out why not, it is going to be a configuration mistake; try searching for Eclipse tutorials that describe how to deploy stuff to Tomcat from Eclipse and compare what you read to what you're doing yourself. In my experience it never works properly out of the box to be honest, there is always some mistake in the deployment assembly, build path, etc.
I don't know if this will help, but you can try creating a very simple SOP project and see if that works on both machines. It might give you some ideas on how to solve your problem. Another possibility is to create a brand new project and copy your java code and configuration files into it. This may (or may not) eliminate any IDE configuration issues that is in the way.