I suspect possible corruption of the VM file in a Mavericks virtual machine. The initial symptom is that Finder shows many folders as empty that Terminal shows to contain the correct files. (Restarting Finder sometimes corrects this.) Disk utility reports no serious permissions issues, but reports file corruption. I cannot be certain whether this is real, or Disk Utility is simply confused by some aspect of the virtual disk. I cannot run it in repair mode because I cannot boot an alternative disk. Has anyone been down this path? Can anyone suggest a way to verify and repair the virtual disk?