Since the update of the Git Client plugin to 1.0.4 git clean (Clean after checkout) doesn't work anymore on Windows build agents. It fails with (the file being different between different tries):

Cleaning workspace

FATAL: Could not delete file C:\JenkinsSlaveHome\slave2\workspace\Somejob\tmp\Store1\trash
org.eclipse.jgit.api.errors.JGitInternalException: Could not delete file C:\JenkinsSlaveHome\slave2\workspace\Somejob\tmp\Store1\trash
at org.eclipse.jgit.api.CleanCommand.call(CleanCommand.java:137)
at org.jenkinsci.plugins.gitclient.JGitAPIImpl.clean(JGitAPIImpl.java:305)
at hudson.plugins.git.GitAPI.clean(GitAPI.java:248)
at hudson.plugins.git.GitSCM$4.invoke(GitSCM.java:1213)
at hudson.plugins.git.GitSCM$4.invoke(GitSCM.java:1196)
at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2348)
at hudson.remoting.UserRequest.perform(UserRequest.java:118)
at hudson.remoting.UserRequest.perform(UserRequest.java:48)
at hudson.remoting.Request$2.run(Request.java:326)
at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: Could not delete file C:\JenkinsSlaveHome\slave2\workspace\Gerrit-FieldWorks-Win-any-develop-debug\tmp\Store1\trash
at org.eclipse.jgit.util.FileUtils.delete(FileUtils.java:142)
at org.eclipse.jgit.api.CleanCommand.call(CleanCommand.java:132)
... 14 more