'06 Publish to a folder  - copies all my sites to that folder

I have tried to publish the site at the top of the top of the Site Organizer list, but it saves all three different sites to the folder. Is this normal?
Also one of my new sites when published, to Mac of to folder and posted, looses the enter link and the email link on the first page. If I publish from page two, the home page, all the links work fine.
thxs

When I published to a folder and tried to upload via cyberduck / ftp / domain, I was getting errors.
Solution: I isolated the "domains.sites" file, copied it, reopened the copy by launching from that copied file. I then removed the other sites that were second and third inline in the site organizer. Resaved, and published to folder, then uploaded the contents. This worked perfectly.
Do you think I need to do this or have you had success leaving all of the different sites in the one domain.sites file?

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