Emre,
I think you have the same problem we did; XMLs exported from a legacy system were missing the namespace so to BizTalk they were all the same. As we needed to process several XMLs at once, our solution was to split off the metadata from the XML so there were two inbound schemas. Works like a charm! The inbound schema with the metadata goes nowhere, the schema with the data gets processed.
I have some pics but this thing won't let me paste them. Let me figure this out and hopefully I can help you.