Phil,
If you have a train on each track in staging, you need to either add another "virtual" empty track in staging for the train to return to. Or change the build mode to "Aggressive" and select the option to "Make the departure track available after train is built".? This tells the program to reuse a staging track even if the train hasn't departed.? Here's the link to the help:
http://jmri.sourceforge.net/help/en/package/jmri/jmrit/operations/Operations.shtml#SettingsOptions
Dan