"Cleaning directory" is run when it shouldn't

Our workarea is wiped out whenever we start a newly configured bamboo build. This is not what we expected as we did not Force Clean Build. But subsequence run on the plan will be fine, the workarea will not be wipe. I have set the priority to be critical as we are migrating bamboo to another server on friday and don't wish that our hundreds of workarea being wipe out.

Saw this ticket but there's no resolution. I thought it should be fixed by version 4.2.1
BAM-10037 "Cleaning directory" is run when it shouldn't

Log file
08-Jan-2013 23:53:54 Build BRANCH-MFGEE2-GENDOC-3 started building on agent coli21.qad.com
08-Jan-2013 23:53:54 Build working directory is /dr01/bamboo-agent-home/xml-data/build-dir/BRANCH-MFGEE2-GENDOC
08-Jan-2013 23:53:54 Cleaning directory /dr01/bamboo-agent-home/xml-data/build-dir/BRANCH-MFGEE2-GENDOC
08-Jan-2013 23:54:47 Unable to clean source directory '/dr01/bamboo-agent-home/xml-data/build-dir/BRANCH-MFGEE2-GENDOC' Unable to delete directory /dr01/bamboo-agent-home/xml-data/build-dir/BRANCH-MFGEE2-GENDOC/build/work/qra.
08-Jan-2013 23:54:48 Executing build BRANCH-MFGEE2-GENDOC-3
08-Jan-2013 23:54:48 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
08-Jan-2013 23:54:48 Running preRetrieveSourceCode task...
08-Jan-2013 23:54:48 Clean checkout enforced by repository configuration
08-Jan-2013 23:54:48 Cleaning build directory '/dr01/bamboo-agent-home/xml-data/build-dir/BRANCH-MFGEE2-GENDOC'
08-Jan-2013 23:54:48 Updating source code to revision: 27239
08-Jan-2013 23:54:48 Working directory '/dr01/bamboo-agent-home/xml-data/build-dir/BRANCH-MFGEE2-GENDOC' is empty. Checking out SVN URL 'http://subversion.qad.com/svn/erp_repository/branches/projects/mfgee2'
08-Jan-2013 23:54:48 Clean checkout enforced by repository configuration
08-Jan-2013 23:54:48 Cleaning build directory '/dr01/bamboo-agent-home/xml-data/build-dir/BRANCH-MFGEE2-GENDOC'
08-Jan-2013 23:54:48 Updating source code to revision: 27239