copying files one drive another prompts duplicate

I proceeded to copy about 250gigs of files from one drive to another and a message came up stating it found a duplicate copy and asking me how to resolve it whether to keep one, the other or both. When I first saw it, I decided, not knowing what I was doing, to keep both. Well, it duplicated everything and tagged suffix of "(2)" on each file. Now I have about 500gigs of duplicates!
Well, instead of going thru each folder and deleting the files with the "(2)", I decided to delete the whole mess and re-copy it over this time telling it to keep the top one in the message box.
This was confusing. Why would it come up saying it found a duplicate?? I know there's lots of cool stuff in Vista, but this thing's got me by the family jewels...
Ace

Oops, meant to add it's 5270, x64.
Downloading the new one now...
Ace