Ok, so an error like that where it says a core definition of the document is missing isn't great to see and could perhaps be related to an outdated OData library. I just tested this on my server and wasn't able to replicate it...what query type is the getFileList query template; sounds like an XacuteQuery. If so is it possible that in your transaction the output xml response never gets set or the XML isn't in proper Illuminator format? This would kill the conversion from MII Illuminator XML to OData JSON and could also cause this error.
Hope this helps,
Sam