The configuration in the magnolia.properties file:
magnolia.author.key.location=WEB-INF/config/default/keypair.properties

should create the file 'keypair.properties' relative within the WEB-INF lib folder.
So correct would be:
apache-tomcat-6.0.32/webapps/magnoliaAuthor/WEB-INF/config/default/keypair.properties

But the file gets created in:
apache-tomcat-6.0.32/bin/WEB-INF/config/default/keypair.properties

There for depending on the write rights on the bin folder of the the file can't be created. Usually the webapplication process doesn't have write writes to tomcat's bin folder -> activation fails.