Are you starting Eclipse thruogh the Visual COBOL icon installed on your desktop or are you starting a different version of Eclipse that may have already been installed on your computer?
Visual COBOL for Eclipse installs it's own copy of Eclipse 3.7 and then installs into it.
If you wish for Visual COBOL to be installed into a preexisting version of Eclipse then there are some additional setup requirements that are covered in the same readme document that I mentioned previously.
What Linux version are you running?