I have recently been creating some flat file schemas using the BizTalk Server 2009 Flat File Schema Wizard.  I have then been mapping these flat file schemas to a "normal" xml schema format.

I have not previsouly had any cause to map flat files and ran into some trouble when testing the first of these flat file maps; with an instance of the flat file as the source it threw an XSL transform error:

Test Map.btm: error btm1050: XSL transform error: Unable to write output instance to the following <file:///C:\Documents and Settings\sbrierley\Local Settings\Temp\_MapData\Test Mapping\Test Map_output.xml>. Data at the root level is invalid. Line 1, position 1.

Due to the complexity of the map in question I decided to created a small test map using the same source and destination schemas to see if I could pinpoint the problem. 

Although the source message instance vaildated correctly against the flat file schema, when I then tested this simplified map I got the same error.

After a time of fruitless head scratching and some serious google time I figured out what the problem was.

Looking at the map properties I noticed that I had the test map input set to "XML" - for a flat file instance this should be set to "native".