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Are you using a WAR file or exploded format? If you have a WAR file (without the properties file), the servlet container may be deploying the WAR each time, overwriting your file. Either remove the WAR from the deployment area, or add the properties file to the WEB-INF/classes in the WAR.

If this isn't your problem, then I'm puzzled like you probably are why this would happen. Which container are you using?