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I've replicated the problem and my suggestion regarding the build definition is not likely to work. I have though figured out how to configure the project so that it will load into non-nested directories.
In the section "Advanced Project Options" click the advanced settings button
Check the box "Use custom workspace" it will expand a section to supply workspace paths for the main build and the sub-builds.
In the "Directory" textbox, put an absolute path and a directory in which to load for the main build.
ie. /data/demeter/dev/jenkins-build/jobs/RunAsfTests10/workspace/mainJob
In the "Directory for sub-builds" textbox, put the same absolute path minus the directory for the main build followed by /${JOB_NAME}
i.e. /data/demeter/dev/jenkins-build/jobs/RunAsfTests10/workspace/${JOB_NAME}
The JOB_NAME is a variable populated by Jenkins, there may be nicer variables, but I haven't found them. The other key point is to use an absolute path for each directory. The use of the variable will result in each of the sub jobs having their own directory.