Why does my time machine backup not copy properly?

I have two external hard drives that are both the same 2TB portable external from Toshiba.

I've tried copying my old time machine backups using these steps:

http://support.apple.com/kb/ht5096

Yet folders keep appearing outside the root folder "backups.backupdb"

The folders that appear are backup folders (which would be located inside the root folder)

I've followed the steps by apple very percisely...

My best clue as to why this is happening is:

The old time machine backups rely on WD's smartware. (And the new one doesn't)

I also get some errors that involve files that can't be copied.

The one that happens before the folders get skewed is similar to this upcoming one, but has to do with a file called "DS_Store"

"The Finder can't complete the operation because some data in "Team Fortress 2 content.gcf" can't be read or written.

(Error code - 36)"

Here are a couple of other error messages I get:

"The operation can't be completed because one or more required items can't be found.

(Error code -43)"

"the operation can't be completed because an unexpected error occured.

(Error code -50)"

I have had a couple more... But I unfortunately forgot to notate them....

That being said, they're all similar in nature to this.

Has anyone experienced similar issues?

If it helps at all.... There is about 956 GB of backup data being copied!