I setup a development environment with Windows 8 and Ubuntu as a virtual machine. For that I use VirtualBox.
I also manage to create a shared folder in VirtualBox.
I have a similar environment. Apparently the Virtualbox (vagrant) synchronisation has problems when renaming or moving files, which happens when updating modules.
If you do a file listing (ls -alhp) on the command line and see ??? for the file permissions, then it is time to reboot your virtualbox. This will set the permissions to valid values. Then use the --no-bin-links option when installing a module.