I ran into this trouble while moving JoomlaHacks.com to a new server. All of sudden, SEF stopped working. I'm sure the server has apache mod_rewrite and there's already one site that has SEF turned on and working properly.
One thing I realized though is that the domain has not propageted yet, so I have to use the reseller domain and access the website via "my_server_domain.com/~account". Using this means the site is in ~account sub-folder.
Solution:
Edit you .htaccess file and uncomment RewriteBase and put the sub-folder. So in my case, it would be:
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