Every time I copy something to my server, the first time it fails and I have to recopy it.  The thing is even though the first copy fails, part of the file is copied over so when I recopy it, I'm prompted to overwrite the existing file.  This happens every single time.  Anyone know why this happens?

There might be something obvious but nothing I'm aware of. Can you give us more to work with? Syslog at a minimum, any error messages you see at the client and server side, whether you're copying to a user or disk share, from windows or what, to SMB or NFS, etc...

Is the target disk spun down?

What are you using to copy with?  I would use Teracopy, it also has the ability to verify copies have the same hash as the original.  I never have issues copying with it, even when the target disks are spun down (which could be the issue). 

I use Teracopy and I'm not sure if the disks are spun down since this happens even when I first start up the server.  I'm just simply copying and pasting the ISOs from my Vista PC to the mapped unRaid drive.