copy protected game saves cannot be transfered/backup to ext drives by any means. if you want to back it up you have to you the ps3's backup utility and it can only be restored to the original ps3.
are you using WD Caviar green drive? if yes, than im very sad to say that you have made a very bad choice. the caviar green drives is the worst choice possible if you want to use it as int hdd for ps3 (or even as ext to play games from).
read the following sites regarding the issue:
next time do some research before you buy. if you want to buy a new ps3 hdd... be safe... and buy the same hdd type as the stock hdd. i've gone out of my way to search the internet about these. please don't hate me. i might be wrong though about all these.
if the problem is solved, please give some details on how you have solved it so others can benefit from you experience. thanks