Can references from the base project be removed from the build projects classpaths?

I have a project with the following structure:

_CSBuilder (this contains the build.xml)
   + lib
   + workspace
      + CommonUtils
      + ESBLibraries
      + ... (other projects)

The idea is to build the projects under the "workspace" folder, which are checked out from our CMDB.

Im using the last release from the Hudson link.

However when I run the build.xml, I receive the following:

BUILD FAILED
C:\_CSBuilder\_CSBuilder\build.xml:456: The following error occurred while executing this line:
C:\_CSBuilder\_CSBuilder\build.xml:459: The following error occurred while executing this line:
C:\_CSBuilder\_CSBuilder\build.xml:476: The following error occurred while executing this line:
C:\_CSBuilder\_CSBuilder\build.xml:490: The following error occurred while executing this line:
C:\_CSBuilder\_CSBuilder\build.xml:272: org.ant4eclipse.lib.core.exception.Ant4EclipseException: Could not create jar file from file 'C:\_CSBuilder\_CSBuilder\.project'.

Not sure why the compile task is trying to include the references to the _CSBuilder project (which only contains the build.xml) in the compilation of the CommonUtils project.

Is there a way to remove such reference from the executeJdtProject properties?

Thanks in advance for your help!

Note: After doing some tests yesterday, found an interesting thing. When I downloaded the code cleaning all projects the error is appearing. If I downloaded the code then imported the code to eclipse, If I run the script disabling the cleaning, the error does not appear, however I would expect to be able to compile from the clean state.