Ah, yes, that can mess things up. I also cleared the registry of all kinds of references to Apache services etc. as it seems a previous installation hadn't removed them properly.
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Joomla??? You don't need mod-rewrite or htaccess for it;
I do, because my live site has SEF links enabled using Artio - it's got quite complex and I didn't really want to revert to non-SEF links because that would be sure to break some links. But I had to just give up in the end because I couldn't reproduce the same environment locally so mod_rewrite would work properly with Artio...