Copy folders with the same name deletes contents of original folder

When backing up some iTunes songs manually I selected the folders I wanted to copy and copied them, then I pasted them into my backup folder.
I got the warning windows about folders having the same name, I could only cancel or replace. So I clicked replace. Then when I checked inside one of the destination folders the original contents of the folder has been erased and only the new files are left.
Has the way Snow Leopard deals with copying folders changed? As I am sure this did not happen before I upgraded.
I tried it on the command line with 'cp -aR' and everything worked as expected, but it does not warn that the folder already exists.
How do I get 'cp -aR' functionality out of finder?

After alot more searching it seems mac OS X has always done this, but I never noticed it before.
I can copy my backups over the network with:
cp -aR Music/source_folder /Volumes/server_name/Music/
ditto can be used as well.

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