What ftp/ftpd is running on the machines, i know of several that have ftpd side option to enable/disable showing hidden files through the ftp sessions.
As for the transferring .files, works fine for me on unix/bsd and windows ftpd, dont have/want an xbox though so no idea on that one.
These files are in my experience, for the most part just used by the ftpd for tracking/quota/message stuff and are useless elsewhere. Which is why they are hidden files.
Edit: have to ask, is ".*" or similar in your skiplist?
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