Problems initializing the application

Successfully installed the Wine reference application. Now trying to set up a real one.
The deploy.sh ran fine. (I didn't reuse the port numbers from the Wine ref app.)
When I run initialize_services.sh I get this (addendum #1 below) The only log which has any thing in it, has this: "ERROR: Failed to get instance configuration from IAP Workbench". No one is logged into the Workbench, and it is up and available on it's own port. (And this worked fine for the Wine ref app).
Comparing AppConfig.xml from the Wine ref app, and the new application - the only differences are the ports numbers, and the name of the application.
==== Start addendum #1 ====
Removing existing application provisioning...
[08.07.12 09:23:14] INFO: Removing application. Any active components will be fo
rced to stop.
[08.07.12 09:23:17] INFO: Removing Web Studio config files.
[08.07.12 09:23:17] INFO: [ITLHost] Starting shell utility 'emgr_update_remove_a
ll_settings'.
[08.07.12 09:23:18] INFO: Removing definition for custom component 'ConfigManage
r'.
[08.07.12 09:23:19] INFO: Updating provisioning for host 'ITLHost'.
[08.07.12 09:23:19] INFO: Updating definition for host 'ITLHost'.
[08.07.12 09:23:19] INFO: Removing definition for application 'basenpoload'.
[08.07.12 09:23:20] INFO: Application 'basenpoload' removed.
Setting EAC provisioning and performing initial setup...
[08.07.12 09:23:20] INFO: Checking definition from AppConfig.xml against existin
g EAC provisioning.
[08.07.12 09:23:21] INFO: Setting definition for application 'basenpoload'.
[08.07.12 09:23:21] INFO: Setting definition for host 'ITLHost'.
[08.07.12 09:23:21] INFO: Setting definition for host 'MDEXHost'.
[08.07.12 09:23:21] INFO: Setting definition for host 'webstudio'.
[08.07.12 09:23:21] INFO: Setting definition for script 'BaselineUpdate'.
[08.07.12 09:23:21] INFO: Setting definition for script 'PartialUpdate'.
[08.07.12 09:23:21] INFO: Setting definition for script 'ConfigUpdate'.
[08.07.12 09:23:21] INFO: Setting definition for custom component 'ConfigManager'.
[08.07.12 09:23:21] INFO: Updating provisioning for host 'ITLHost'.
[08.07.12 09:23:21] INFO: Updating definition for host 'ITLHost'.
[08.07.12 09:23:22] INFO: Setting definition for component 'Forge'.
[08.07.12 09:23:22] INFO: Setting definition for component 'PartialForge'.
[08.07.12 09:23:22] INFO: Setting definition for component 'Dgidx'.
[08.07.12 09:23:23] INFO: Setting definition for component 'Dgraph1'.
[08.07.12 09:23:23] INFO: Setting definition for component 'Dgraph2'.
[08.07.12 09:23:24] INFO: Setting definition for component 'LogServer'.
[08.07.12 09:23:24] INFO: Setting definition for script 'DailyReports'.
[08.07.12 09:23:24] INFO: Setting definition for script 'WeeklyReports'.
[08.07.12 09:23:24] INFO: Setting definition for script 'DailyHtmlReports'.
[08.07.12 09:23:25] INFO: Setting definition for script 'WeeklyHtmlReports'.
[08.07.12 09:23:25] INFO: Setting definition for component 'WeeklyReportGenerator'.
[08.07.12 09:23:25] INFO: Setting definition for component 'DailyReportGenerator'.
[08.07.12 09:23:26] INFO: Setting definition for component 'WeeklyHtmlReportGenerator'.
[08.07.12 09:23:26] INFO: Setting definition for component 'DailyHtmlReportGenerator'.
[08.07.12 09:23:26] INFO: Definition updated.
[08.07.12 09:23:26] INFO: Updating Oracle Endeca Workbench configuration...
[08.07.12 09:23:26] INFO: Downloading config files from Web Studio.
[08.07.12 09:23:26] INFO: [ITLHost] Starting shell utility 'emgr_update_get_ws_settings'.
[08.07.12 09:23:27] SEVERE: Utility 'emgr_update_get_ws_settings' failed. Refer to utility logs in [ENDECA_CONF]/logs/shell on host ITLHost.
Occurred while executing line 5 of valid BeanShell script:
2|
3| if (ConfigManager.isWebStudioEnabled()) {
4| log.info("Updating Oracle Endeca Workbench configuration...");
5| ConfigManager.updateWsConfig();
6| log.info("Finished updating Oracle Endeca Workbench.");
7| }
8|
[08.07.12 09:23:27] SEVERE: Caught an exception while invoking method 'run' on object 'InitialSetup'. Releasing locks.
Caused by java.lang.reflect.InvocationTargetException
sun.reflect.NativeMethodAccessorImpl invoke0 - null
Caused by com.endeca.soleng.eac.toolkit.exception.AppControlException
com.endeca.soleng.eac.toolkit.script.Script runBeanShellScript - Error executing valid BeanShell script.
Caused by com.endeca.soleng.eac.toolkit.exception.EacComponentControlException
com.endeca.soleng.eac.toolkit.utility.Utility run - Utility 'emgr_update_get_ws_settings' failed. Refer to utility logs in [ENDECA_CONF]/logs/shell on host ITLHost.
==== End addendum #1 ====

Found out what I did wrong. When prompted for Tools/Workbench port, when running deploy.sh, I used a new one. I was thinking that a new Workbench was spun up for each application. Once I went back to the port I set up for the Wine referenece application the initiallize_services.sh ran with no errors.

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