I've experienced a number of problems with install wizard, some of which I can consistently reproduce while the CRJZS0040E errors seems to be repeatible on the first run through the installation Wizard, but doesn't occur if you start the installation wizards again.

I've tried to diagnose them as much as possible to help you replicate them.

I've failed in the Finalise Application set for the Change and Configuration Management(/ccm) application.

None of the log files contain any reference to the above CRJZS0040E error when I look in the:

C:\Program Files\IBM\JazzTeamServer\server\tomcat\logs
C:\Program Files\IBM\JazzTeamServer\server\logs directory.

the catalina.log contains this error

28/02/2011 21:27:15 org.dojotoolkit.zazl.RhinoClassLoader loadJS
SEVERE: ClassNotFoundException while loading javascript
java.lang.ClassNotFoundException: com.ibm.team.lpa.app.ui.internal.wizard.nls.en-au.SetupWizardMessages

I uninstalled and repeated the installation and this time captured the URL's as the installation wizard process progressed.

Again it failed on the first time through the wizard and below is the URL's as it progresses:

https://test.testing2dot0.com:9443/jts/setup#/steps/12&h=664&cf=0&cn=0&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/13&h=627&cf=0&cn=0&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/14&h=589&cf=0&cn=1&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/15&h=682&cf=0&cn=1&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/16&h=664&cf=0&cn=0&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/16&h=664&cf=0&cn=1&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/17

At this point the URL refreshed and displayed the following - Note that 17 has disappeared from the URL string after the URL refreshed

https://test.testing2dot0.com:9443/rm/&h=831&cf=0&cn=0&cp=1&cc=1

On rerunning the installation wizard, the following list of URLs were displayed

https://test.testing2dot0.com:9443/jts/setup#/steps/7
https://test.testing2dot0.com:9443/jts/setup#/steps/8&h=627&cf=0&cn=0&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/9
https://test.testing2dot0.com:9443/jts/setup#/steps/9&h=589&cf=0&cn=1&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/10&h=686&cf=0&cn=1&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/11
https://test.testing2dot0.com:9443/jts/setup#/steps/11&h=288&cf=0&cn=1&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/12
https://test.testing2dot0.com:9443/jts/setup#/steps/12&h=627&cf=0&cn=0&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/13
https://test.testing2dot0.com:9443/jts/setup#/steps/13&h=589&cf=0&cn=1&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/14
https://test.testing2dot0.com:9443/jts/setup#/steps/14&h=682&cf=0&cn=0&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/15 delay of about 3 seconds before
https://test.testing2dot0.com:9443/jts/setup#/steps/15&h=288&cf=0&cn=1&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/16
https://test.testing2dot0.com:9443/jts/setup#/steps/16&h=831&cf=0&cn=0&cp=1&cc=1
https://test.testing2dot0.com:9443/jts/setup#/steps/17
https://test.testing2dot0.com:9443/jts/setup#/steps/17&h=568&cf=0&cn=1&cp=1&cc=1

I also observed that some URL's didn't display the /steps/XX URL pattern before refreshing, instead displaying the full /steps/XX&h={rest of the URL pattern}

Other things found while investigating this issue are listed below:

if I use Firefox/3.6.13 the finalise button for the requirements Management section never gets enabled. But if I use IE 8.0.6001 then button does become enabled.

if I repeat the setup and don't stop the server I run into Caching errors for the Configure Data Warehouse settings for Quality Manager and Configuration Manager where the value that gets repopulated is conf/jts/derby/warehouseDB. This can be fixed by changing the value to conf/qm/derby/warehouseDB and conf/ccm/derby/warehouseDB respectively