I'm pretty sure if it's using dflt.fos that means Arbortext did not find the stylesheet for your DTD, meaning your custom FOSI is not loaded. You should have an APTCUSTOM environment variable that is pointing to the custom folder containing all your doctypes, so that is a good place to start debugging .. or you can have a look at "Select Stylesheets" under the Format menu. Help->Session->Document will also show some helpful information.
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