Code:
RewriteEngine On
RewriteBase /wiki/
RewriteCond %{REQUEST_URI} !^/wiki/index.php$
RewriteCond %{REQUEST_URI} !^/wiki/index.php/
#RewriteRule ^(.*)$ index.php?%{QUERY_STRING} [L]
#RewriteRule ^(.*)$ index.php [L]
responding to various points:
changes to htaccess files are immediate. there's nothing to wait for before your changes take effect.
(When I mentioned "changes not propagated yet" earlier, I was referring to any changes to the actual apache vhost configuration, which is what assigning document roots via goDaddy's CP [should] do. There's no reason those changes shouldn't be immediate as well, but I can imagine them being lazy about it.)
Directory names with dots also shouldn't be a problem (at least, on a Linux server) but again: it's goDaddy. I have no idea what kind of hacky crap they might pull behind the scenes.
Multiple name servers (or maybe load balancers): That's a possibility I hadn't thought of. If there was a problem syncing your changes (or some changes they made, say, three months ago), then that could explain why it's intermittent. Unfortunately, this is something they would have to check (and I doubt they would).
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