We are facing the same issue (on Linux as original reporter).

Jenkins ver Jenkins ver. 1.509.4 LTS
OS ver Scientific Linux release 6.4 (Carbon)

The same stacktrace as above.

Jan 01, 2014 7:05:37 PM jenkins.model.PeepholePermalink updateCache
WARNING: Failed to update hudson.model.FreeStyleProject@6d5d2cc[prototype load] lastStableBuild permalink for prototype load t2mg0i1lkvibf4v07yw184j0m0j6yk2m-1383593938@qa-9
8prototype-1.na.getgooddata.com
java.nio.file.NoSuchFileException: /var/lib/jenkins/jobs/prototype load/builds/lastStableBuild.tmp
        at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
        at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
        at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
        at sun.nio.fs.UnixFileSystemProvider.readSymbolicLink(UnixFileSystemProvider.java:495)
        at java.nio.file.Files.readSymbolicLink(Files.java:1382)
        at sun.reflect.GeneratedMethodAccessor41.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at hudson.Util.resolveSymlink(Util.java:1216)
        at jenkins.model.PeepholePermalink.writeSymlink(PeepholePermalink.java:169)
        at jenkins.model.PeepholePermalink.updateCache(PeepholePermalink.java:137)
        at jenkins.model.PeepholePermalink$RunListenerImpl.onCompleted(PeepholePermalink.java:214)
        at hudson.model.listeners.RunListener.fireCompleted(RunListener.java:199)
        at hudson.model.Run.execute(Run.java:1642)
        at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46)
        at hudson.model.ResourceController.execute(ResourceController.java:88)
        at hudson.model.Executor.run(Executor.java:237)


Bigger log fragment here - 140107-LZA-J19741-log-fragment.log

Statistic per day on our Jenkins instance:

[root@jenkins-1509:/var/lib/jenkins/logs] zgrep -c "WARNING: Failed to update hudson.model.FreeStyleProject" jen* | sort -r
jenkins.log:23 (20140106)
jenkins.log-20140104.gz:26
jenkins.log-20140101.gz:22
jenkins.log-20131227.gz:18
jenkins.log-20131221.gz:23
jenkins.log-20131219.gz:1

IMO it has nothing to do with windows platform.

=> Reopening

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