Files empty after moving with FTP

I have a strange bug within my WordPress theme.

After I copy normal files from my local machine (whatever file, functions.php, styles.css or any other) the file gets empty on the server, with no content and I can see the size of 0mb.

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On the backend, wp-admin works normally, I have previousely received some caching error but that its.

Any ideas?

P.s. I am using WP 3.1

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