After a remote trigger the git init command failed with the following exception:

Started on 5/03/2014 1:42:45 PM
Using strategy: Default
[poll] Last Built Revision: Revision 6c615c2d4570d1aa9288afd73588a7328073e832 (origin/master)
using .gitcredentials to set credentials
Could not remove the credential section from the git configuration
FATAL: hudson.plugins.git.GitException: Command "git init" returned status code 128:
stdout:
stderr: fatal: cannot copy 'C:\Program Files\Git/share/git-core/templates/description' to 'C:/DOCUME~1/!SYSCA~1/LOCALS~1/Temp/.git/description': File exists

ha:AAAAWB+LCAAAAAAAAP9b85aBtbiIQSmjNKU4P08vOT+vOD8nVc8DzHWtSE4tKMnMz/PLL0ldFVf2c+b/lb5MDAwVRQxSaBqcITRIIQMEMIIUFgAAckCEiWAAAAA=hudson.util.IOException2: hudson.plugins.git.GitException: Command "git init" returned status code 128:
stdout:
stderr: fatal: cannot copy 'C:\Program Files\Git/share/git-core/templates/description' to 'C:/DOCUME~1/!SYSCA~1/LOCALS~1/Temp/.git/description': File exists

at hudson.plugins.git.GitSCM.compareRemoteRevisionWith(GitSCM.java:459)
at hudson.scm.SCM._compareRemoteRevisionWith(SCM.java:356)
at hudson.scm.SCM.poll(SCM.java:373)
at hudson.model.AbstractProject._poll(AbstractProject.java:1581)
at hudson.model.AbstractProject.poll(AbstractProject.java:1490)
at hudson.triggers.SCMTrigger$Runner.runPolling(SCMTrigger.java:462)
at hudson.triggers.SCMTrigger$Runner.run(SCMTrigger.java:491)
at hudson.util.SequentialExecutionQueue$QueueEntry.run(SequentialExecutionQueue.java:118)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
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: hudson.plugins.git.GitException: Command "git init" returned status code 128:
stdout:
stderr: fatal: cannot copy 'C:\Program Files\Git/share/git-core/templates/description' to 'C:/DOCUME~1/!SYSCA~1/LOCALS~1/Temp/.git/description': File exists

at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1173)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1150)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1146)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1142)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandWithCredentials(CliGitAPIImpl.java:1035)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandWithCredentials(CliGitAPIImpl.java:988)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandWithCredentials(CliGitAPIImpl.java:979)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.getHeadRev(CliGitAPIImpl.java:1526)
at hudson.plugins.git.GitSCM.compareRemoteRevisionWithImpl(GitSCM.java:489)
at hudson.plugins.git.GitSCM.compareRemoteRevisionWith(GitSCM.java:457)
... 13 more
Done. Took 0.5 sec
No changes

The second time it failed with a similar exception:

Started on 5/03/2014 1:46:38 PM
Using strategy: Default
[poll] Last Built Revision: Revision 6c615c2d4570d1aa9288afd73588a7328073e832 (origin/master)
using .gitcredentials to set credentials
Could not remove the credential section from the git configuration
FATAL: hudson.plugins.git.GitException: Command "git init" returned status code 128:
stdout:
stderr: fatal: cannot copy 'C:\Program Files\Git/share/git-core/templates/hooks/post-update.sample' to 'C:/DOCUME~1/!SYSCA~1/LOCALS~1/Temp/.git/hooks/post-update.sample': File exists

ha:AAAAWB+LCAAAAAAAAP9b85aBtbiIQSmjNKU4P08vOT+vOD8nVc8DzHWtSE4tKMnMz/PLL0ldFVf2c+b/lb5MDAwVRQxSaBqcITRIIQMEMIIUFgAAckCEiWAAAAA=hudson.util.IOException2: hudson.plugins.git.GitException: Command "git init" returned status code 128:
stdout:
stderr: fatal: cannot copy 'C:\Program Files\Git/share/git-core/templates/hooks/post-update.sample' to 'C:/DOCUME~1/!SYSCA~1/LOCALS~1/Temp/.git/hooks/post-update.sample': File exists

at hudson.plugins.git.GitSCM.compareRemoteRevisionWith(GitSCM.java:459)
at hudson.scm.SCM._compareRemoteRevisionWith(SCM.java:356)
at hudson.scm.SCM.poll(SCM.java:373)
at hudson.model.AbstractProject._poll(AbstractProject.java:1581)
at hudson.model.AbstractProject.poll(AbstractProject.java:1490)
at hudson.triggers.SCMTrigger$Runner.runPolling(SCMTrigger.java:462)
at hudson.triggers.SCMTrigger$Runner.run(SCMTrigger.java:491)
at hudson.util.SequentialExecutionQueue$QueueEntry.run(SequentialExecutionQueue.java:118)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
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: hudson.plugins.git.GitException: Command "git init" returned status code 128:
stdout:
stderr: fatal: cannot copy 'C:\Program Files\Git/share/git-core/templates/hooks/post-update.sample' to 'C:/DOCUME~1/!SYSCA~1/LOCALS~1/Temp/.git/hooks/post-update.sample': File exists

at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1173)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1150)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1146)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1142)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandWithCredentials(CliGitAPIImpl.java:1035)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandWithCredentials(CliGitAPIImpl.java:988)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandWithCredentials(CliGitAPIImpl.java:979)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.getHeadRev(CliGitAPIImpl.java:1526)
at hudson.plugins.git.GitSCM.compareRemoteRevisionWithImpl(GitSCM.java:489)
at hudson.plugins.git.GitSCM.compareRemoteRevisionWith(GitSCM.java:457)
... 13 more
Done. Took 0.31 sec
No changes

Both times the .git folder had been deleted before triggering.