Microsoft backup restore of windows server 2008 R2 created copy of all files

We did a Microsoft backup restore of windows server 2008 R2 (not SQL Server).  That created a copy of all files in all dirs.  For example, it created a copy of all files or directories in the windows directory.  For the net beans install, for example, for every single file "x", it created "copy of x" in the same directory.  This corrupted the iis because of all the copies.  Same thing with some of the other applications...they didn't work.  Once we deleted the copies, for example, iis worked again.  Same thing with net beans.  We're still working on some of the other programs. 

So, next time we do a restore, we want to prevent "copy of x" for everything to be created.  How do we do that?  Any ideas what we did or didn't do?

Thanks,

M