When a stream, or repository workspace, has multiple components where each component has a similar (sub) directory structure (e.g. "build"-folder, containing all build scripts and settings for that component), there's not a setting available that allows the load of these components as root folders in a sandbox.
This means that when the components get loaded, not being root folders, there are directory collisions, which RTC cannot resolve (see log below). This causes the Jenkins Job to fail, even before the actual build steps are reached.

Please introduce a configuration setting that allows components to be loaded as root folders.

Settings Jenkins Job, Team Concert plugin:
==========================================
Disabled: Override global RTC repository connection
Enabled: Just accept and fetch from a build workspace
Enabled: Poll SCM, schedule: H/25 * * * *

Jenkins Job log:
================
Started by an SCM change
[EnvInject] - Loading node environment variables.
Building in workspace C:\Data\IBM\RTC
RTC : checkout...
RTC Checkout : Source control setup
RTC Checkout : Accepting changes into workspace "sys24_Team_Build_Workspace" ...
RTC Checkout : Fetching files to fetch destination "C:\Data\IBM\RTC" ...
FATAL: RTC : checkout failure: Loading the directories in the file system would overwrite/remove existing directories.
Loading the directories in the file system would overwrite/remove existing directories.
/Build (requested to be loaded from both component Build and EPN-uEPN)
/Test (requested to be loaded from both component Build and ActionTools)
/Data (requested to be loaded from both component Build and ActionTools)
/Lib (requested to be loaded from both component Build and ActionTools)

com.ibm.team.build.internal.scm.SourceControlUtility$3: Status WARNING: com.ibm.team.filesystem.client code=2 Loading the directories in the file system would overwrite/remove existing directories. null children=[Status WARNING: com.ibm.team.filesystem.client code=0 /Build (requested to be loaded from both component Build and EPN-uEPN) null Status WARNING: com.ibm.team.filesystem.client code=0 /Test (requested to be loaded from both component Build and ActionTools) null Status WARNING: com.ibm.team.filesystem.client code=0 /Data (requested to be loaded from both component Build and ActionTools) null Status WARNING: com.ibm.team.filesystem.client code=0 /Lib (requested to be loaded from both component Build and ActionTools) null]
at com.ibm.team.build.internal.scm.SourceControlUtility.updateFileCopyArea(SourceControlUtility.java:685)
at com.ibm.team.build.internal.hjplugin.rtc.RepositoryConnection.checkout(RepositoryConnection.java:367)
at com.ibm.team.build.internal.hjplugin.rtc.RTCFacade.checkout(RTCFacade.java:321)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.ibm.team.build.internal.hjplugin.RTCFacadeFactory$RTCFacadeWrapper.invoke(RTCFacadeFactory.java:92)
at com.ibm.team.build.internal.hjplugin.RTCCheckoutTask.invoke(RTCCheckoutTask.java:103)
at com.ibm.team.build.internal.hjplugin.RTCCheckoutTask.invoke(RTCCheckoutTask.java:30)
at hudson.FilePath.act(FilePath.java:904)
at hudson.FilePath.act(FilePath.java:877)
at com.ibm.team.build.internal.hjplugin.RTCScm.checkout(RTCScm.java:836)
at hudson.model.AbstractProject.checkout(AbstractProject.java:1369)
at hudson.model.AbstractBuild$AbstractBuildExecution.defaultCheckout(AbstractBuild.java:676)
at jenkins.scm.SCMCheckoutStrategy.checkout(SCMCheckoutStrategy.java:88)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:581)
at hudson.model.Run.execute(Run.java:1575)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46)
at hudson.model.ResourceController.execute(ResourceController.java:88)
at hudson.model.Executor.run(Executor.java:241)
Contains : 0 /Build (requested to be loaded from both component Build and EPN-uEPN)
Contains : 1 /Test (requested to be loaded from both component Build and ActionTools)
Contains : 2 /Data (requested to be loaded from both component Build and ActionTools)
Contains : 3 /Lib (requested to be loaded from both component Build and ActionTools)
ERROR: RTC : checkout failure: Loading the directories in the file system would overwrite/remove existing directories.
Loading the directories in the file system would overwrite/remove existing directories.
/Build (requested to be loaded from both component Build and EPN-uEPN)
/Test (requested to be loaded from both component Build and ActionTools)
/Data (requested to be loaded from both component Build and ActionTools)
/Lib (requested to be loaded from both component Build and ActionTools)

Finished: FAILURE