Using the "Emulate clean checkout by first deleting unversioned/ignored files, then 'svn update'" svn strategy, we recently had a branch merged into
trunk that added some files. When the Jenkins jobs configured as above
ran against trunk, those added files had their content duplicated.

A quick google suggested it has happened before:

http://grokbase.com/p/lucene/dev/126m8fpw9q/jenkins-lucene-solr-tests-only-4-x-build-137-still-failing