In bug 1055 I used Jetty 6. This time I did the same test with Tomcat 5.5.17.

• Installed Tomcat 5.5.17 (using JDK 1.5 update 6)
• copied magnolia-3.0-rc3-SNAPSHOT.war (build 6449) into {Tomcat install}

  /webapps

• renamed magnolia-3.0-rc3-SNAPSHOT.war to mg6449.war
• started Tomcat
• checked Tomcat error log (stdout_20060921)
  ----> exact same error as with a clean jetty 6 installation!
  The Error message:
  INFO info.magnolia.cms.beans.config.ContentRepository ContentRepository.java(loadRepositories:264) 21.09.2006 20:52:47 Loading workspace:usergroups
  INFO info.magnolia.cms.beans.config.ContentRepository ContentRepository.java(loadRepositories:264) 21.09.2006 20:52:47 Loading workspace:mgnlSystem
  INFO info.magnolia.cms.beans.config.ContentRepository ContentRepository.java(loadRepositories:264) 21.09.2006 20:52:47 Loading workspace:mgnlVersion
  INFO info.magnolia.cms.beans.config.ContentRepository ContentRepository.java(loadRepository:305) 21.09.2006 20:52:47 System : loading JCR magnolia
  INFO info.magnolia.jackrabbit.ProviderImpl ProviderImpl.java(init:143) 21.09.2006 20:52:47 Loading repository at C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\mg6449\${magnolia.repositories.home}\magnolia (config file: C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\mg6449\${magnolia.repositories.jackrabbit.config})
  ERROR info.magnolia.jackrabbit.ProviderImpl ProviderImpl.java(init:176) 21.09.2006 20:52:48 Unable to initialize repository: Configuration file could not be read.: C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\mg6449\${magnolia.repositories.jackrabbit.config} (The system cannot find the file specified)
  org.apache.jackrabbit.core.config.ConfigurationException: Configuration file could not be read.: C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\mg6449\${magnolia.repositories.jackrabbit.config} (The system cannot find the file specified): C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\mg6449\${magnolia.repositories.jackrabbit.config} (The system cannot find the file specified)
  at org.apache.jackrabbit.core.config.ConfigurationParser.parseXML(ConfigurationParser.java:551)
  at org.apache.jackrabbit.core.config.ConfigurationParser.parseRepositoryConfig(ConfigurationParser.java:200)
  at org.apache.jackrabbit.core.config.RepositoryConfig.create(RepositoryConfig.java:140)
  at org.apache.jackrabbit.core.config.RepositoryConfig.create(RepositoryConfig.java:83)
  at org.apache.jackrabbit.core.jndi.BindableRepository.init(BindableRepository.java:134)
  at org.apache.jackrabbit.core.jndi.BindableRepository.create(BindableRepository.java:122)
  at org.apache.jackrabbit.core.jndi.BindableRepositoryFactory.createInstance(BindableRepositoryFactory.java:58)
  at org.apache.jackrabbit.core.jndi.RegistryHelper.registerRepository(RegistryHelper.java:59)
  at info.magnolia.jackrabbit.ProviderImpl.init(ProviderImpl.java:165)

If I look at the INFO (before the error):
Loading repository at C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\mg6449\${magnolia.repositories.home}\magnolia
I interpret that it's loading the repositories at

\webapps\mg6449\repositories\magnolia. However, there is no "\repositories" folder. So I assume it will be created.
The second part of the line reads:
(config file: C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\mg6449\${magnolia.repositories.jackrabbit.config})
looking into the magnolia.properties again, this would mean, that the config file is at
C:\Program Files\Apache Software Foundation\Tomcat 5.5\webapps\mg6449\WEB-INF/config/repo-conf/jackrabbit-derby-search.xml
If I check the location, the file is there. So everything should be ok!
However, now comes the error, that the configuration file COULD NOT BE FOUND (although it's there). If the message is correct, and the file can not be found, even though it's there, then I have the feeling that there must be a problem with the PATH settings.