If you're not using hibernate, and start networkserver using a jvm command, derby.properties file is expected to be in the directory where you start the command from.
Maybe this page is of interest to you: http://wiki.apache.org/db-derby/DatabaseNamesRelativeAbsolute (Note that it is pointless to set derby.system.home in the derby.properties file; the optional derby.properties file would be located in the directory passed on to the java executable with -Dderby.system.home=<path/dir>.) Hth, Myrna