Win7 File Copy Problem

I have a couple of external hard disks connected, 2Tb & 500Gb. The 2Tb
disk has a folder called Music on it with over 4000 folders within it,
each folder is a cd/album. I just spent 6+ hours copying the folder to
the freshly formatted 500Gb drive. It's slightly over 400Gb total. I did
this by right clicking on the folder and drag/dropping it onto the
second drive in the "root" folder and selecting Copy.

At the end of it I received a query to copy 50+ files overwritting what
was already there? ??? Why would it not have already copied them and/or
what are they doing on the original disk in the first place if they have
duplicate names?

In any case, I answered Yes/Allow and then compared both folders on the
two drives. They numbers coming back are not the same. The folder number
is but the # of files is different. It appears somehow the original has
duplicate filenames. I have seen this happen the odd time before also.
The difference appears to be the same number of files.

WTF - seems every version of Windows has become less reliable in it's
most basic of operations. Can't even be sure anymore copying files is
done properly and sure didn't have things like long stalls etc. happen
in XP but sure showed themselves starting with Vista. Often enough,
you'd swear a hard disk has gone offline, e.g. 10-15+ second stalls
before window is filled with file/folder listings etc. That's even
sometimes simply double clicking on a drive icon in MY Computer to open
a drive at the root level.

Now how the hell am I supposed to figure out where the 50+ "extra" files
are on the original disk when there's something like 70,000+ total? I'm
open to suggestions rather than manually searching each and every
folder.

P.S. I have Search etc. all turned off.