Is there a directory in your account for the subdomain? If so, I'd put a file in it like the-domain-name.txt, then go back to the site & refresh to see if it appears.
I'd do the same for other folders until you narrow it down to where it's actually mirroring.
You could also re-save the domain settings to see if that changes anything, even if it's already correct. It's sometimes a fix for the mystery bad_httpd_conf error, so maybe you'll get lucky.
There aren't any .htaccess files floating around in there that could be causing trouble, are there?
If it's not something really simple/obvious that's being overlooked, it will probably end up being a job for support.
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