Currently, the Eclipse Ant builder is not controlled by the "WOLips -> Build" setting in Eclipse's Preferences. You need to explicitly tell it to use your modified wolips.properties file. In your project, open the build.properties file in your project and add the fully-qualified path to your customized wolips.properties file.If you don't build your application for deployment from within Eclipse, then you don't need to follow this step, but you will need to somehow tell your build system where to find the WebObjects frameworks, which I'll leave as an excercise for the reader.
Along with the usual argument that tells ant where the woproject.jar file is, you simply add another argument using the standard java command line property argument. Essentially we set a property telling the build.xml where the wolips properties file is and the build.xml in turn reads in all the properties from that.
$ ant -lib /path/to/woproject.jar -Dwolips.properties /path/to/wolips.533.properties clean build