Windows 2008 R2 - Kernel (System Process PID=4) is locking files and folders for a long time. For example when deleting a file, the file may remain locked for 1 minute or more and only after that be deleted. On another occasions I encountered files or folders I could not delete. ProcMon showed that the System Process was holding a handle to those resources for a couple of minutes and then released them None of the resources I mentioned were system resources, only files and folders installed be me and handled by my applications.
As Dani has already mentioned in the comment:
It's a bug in Windows 7 and likely in Windows Server 2008 (possibly 64bit versions only). It surfaces when you disable Application Experience service.
Re-enabling this service has fixed this problem for me.
A bit more info here as to why it's causing a problem.
List of other SO questions which seem to be related: