Publishing issues using iWeb 3.0.4 (601) on-board FTP loader with 1&1

I've searched and found nothing that looks like this particular problem (could be I didn't use the right keywords, but please no replies telling me to try a search.)
I have 2 websites that I manage on a 1&1 hosting account.
Several days ago, both were publishing properly, and navigating properly from the base domain (stjohnslex.com & forkyle.us). Currently, I'm not sure what's going on.
Somehow, either by my error or a server malfunction the sites began acting strangely. The stjohnslex.com site gave a 404 and the forkyle.us site started directing back to the stjohnslex.com webpage using the forkyle URL. I spent hours on the phone with tech support and as much as I feel like they tried to help me, they couldn't get that iWeb has its own FTP loader.
So here's what happens when I click publish: The forkyle site tends to publish quickly. The stjohnslex site gets to the stage where the little gray publishing pie shows up beside the name but never notes any progress.
When I go to the 1&1 Webspace explorer, all the files appear to be there. Finally in a fit of frustration, I deleted EVERYTHING in my online account and republished the forkyle site, and it appears to be working as intended. The church website still doesn't want to load. I've checked and re-checked my FTP settings, the account name and password, the URL that it's supposed to publish as, the port is set to 21, and the Test Connection tells me everything's good to go. I just can't for the life of me figure out what's going wrong with it.
Any ideas?

The iWeb FTP uploads the folder containing all the website files and an index.html file.
If you upload two websites to the same root folder, one of the index.html files will over write the other.
When you enter the URL...
http://www.domain.com/
.. you are directed to the index.html file which opens the Home or first page of the site whose index.html file resides in the root folder.
I'm only guessing here as I don't know your hosting setup.
Perhaps you need to upgrade your hosting account to accomodate more than on site so that each has its own root folder.
Even the most backward hosting usually offers an extra folder - public_html and WWW - or something like that.

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