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Tempest, I've just realised who you are, remember that little old irc channel back around 10 years ago ?
Yes, if you turn on error reporting ALL on php it will produce warnings with MOST scripts. The thing is, people don't do that in production environments. Warnings are not errors. As for ioncube, fantastic little system, you should try it, ioncube is used by many scripts.
Wordpress writes to doc root when you edit your permalinks, it modifies the .htaccess file. I think you need to tell them about that.
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