This week's book giveaway is in the OO, Patterns, UML and Refactoring forum. We're giving away four copies of Refactoring for Software Design Smells: Managing Technical Debt and have Girish Suryanarayana, Ganesh Samarthyam & Tushar Sharma on-line! See this thread for details.
As you have discovered, the system classpath is not included in web apps.
One way that I have handled similar situations in the past is to identify a location, outside the web app, that the properties file will reside within. I specify this location to the web app as a context parmeter in the deployment descriptor.