Dhaval,
Repeat with me: DTD’s in BizTalk are bad, waaaaay bad.
I would remove any evidence of DTD’s from messages that are traversing through BizTalk as Xml; if you need to include this tag for delivery to an end system, I would suggest using a simple encoding pipeline component to do the work for you, just before BizTalk passes the message to the FTP Adapter.
Funnily enough, I encountered exactly the same problem on BizTalk 2004 some years ago and wrote a component to do this – see Add DOCTYPE Declaration Encoding Pipeline Component (version 1.0) on the downloads page of my blog.
Bear in mind that this component was written for the .Net 1.1 runtime, so will need to be recompiled for BizTalk 2006.
Rgds, Nick.