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Are you using the FTP mode or the direct files mode? Using the direct file writes is bound to give you problems, as you are not using your root FTP account. For more background information on how users, groups, ownerships and permissions work please take a look at the Security introduction chapter and - most importantly - the How your web server works chapter. This material is pretty tight, so you might want to give it two or three readings until you get a firm understanding of those concepts. Other people who read it have told me that after 2-3 readings they gained a much better understanding and were able to sort out most permissions problems themselves.