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It appears that you're using Windows on the client side, right? If so, those ^M chars are the nl/cr issues between Windows and
Unix. I can't tell you how to get rid of them - I'm a linux user - other than open the file in vi on the server side and do:
:%s/^V^M//g
That's: <ctrl>V<ctrl>M (carrots will be create by hoilding down the ctrl key and hitting the letter).
I know several FTP clients allow you to upload as a unix file, and I think Dreamweaver does.
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