On my system (Vista), powershell shows the c:\ drive as having both hidden and system attributes set.
PS C:\Users\michael.DOMAIN> Get-Item c:\
Directory:
Mode LastWriteTime Length Name
---- ------------- ------ ----
d--hs 8/18/2009 12:19 PM <DIR> C:\
After copying the files, you can use attrib to fix them. Check out attrib /? for details.