This seems quite random. I have the backup 1.6 plugin and here is what happens. I am using the "backup configurations only" option and not shutting down Hudson (because it takes too long!). There is no apparent reason why it fails on the listed config.xml - it is stable and not being changed.
.. (many succesfully accessed config files) ..
[DEBUG] jobs/CTX_Nightly_Smoke_Tests_Prepare_Build/modules/com.cisco.txbu.ctc$ctc-eca/config.xml file
[DEBUG] jobs/CTX_Nightly_Smoke_Tests_Prepare_Build/modules/com.cisco.txbu.ctc$CommonCC/config.xml file
[DEBUG] jobs/CTX_Nightly_Smoke_Tests_Prepare_Build/modules/com.cisco.txbu.ctc$ctc-admin/config.xml file
[ERROR] org.codehaus.plexus.archiver.ArchiverException: Failed to read filesystem attributes for: /opt/hudson/conf/jobs/CTX_Nightly_Smoke_Tests_Prepare_Build/modules/com.cisco.txbu.ctc$ctc-admin/config.xml
org.jvnet.hudson.plugins.backup.BackupException: java.io.IOException: Unable to add jobs/CTX_Nightly_Smoke_Tests_Prepare_Build/modules/com.cisco.txbu.ctc$ctc-admin/config.xml
at org.jvnet.hudson.plugins.backup.utils.BackupEngine.doBackup(BackupEngine.java:115)
at org.jvnet.hudson.plugins.backup.utils.BackupTask.run(BackupTask.java:130)
at java.lang.Thread.run(Thread.java:619)
Caused by: java.io.IOException: Unable to add jobs/CTX_Nightly_Smoke_Tests_Prepare_Build/modules/com.cisco.txbu.ctc$ctc-admin/config.xml
at org.jvnet.hudson.plugins.backup.utils.BackupEngine.handleFile(BackupEngine.java:90)
at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:367)
at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:364)
at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:364)
at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:364)
at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:364)
at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:335)
at org.jvnet.hudson.plugins.backup.utils.BackupEngine.doBackup(BackupEngine.java:113)
... 2 more
[ INFO] Cancel hudson shutdown mode
I should have also mentioned that the scm-polling.log file does exist and is readable.