Mark,
This is a restriction of the Eclipse platform. Your WEB-INF/classes is your output folder, it is scrubbed before every project build. Your properties files should be in your /src folder in the appropriate package, when your project is built, they are copied across into the output folder into the proper location.
Also you should check the classes/* contents into CVS, they can be generated. <– NOTE, this is just good practice, not a requirement of anything.