Yahooo !!! i resolved the issue, since it was a runtime exception and its source was Microsoft.XLANGs.Engine
Target Site: System.Xml.XmlDocument AggregateXmlDocuments, i disassemble the dll and looked for this particular method and found that the exception will occur if any of the input xml has the xml declearation and that is because it considers xml decleartion as a root and hence it says
“Error:Invalid input/output document into/from the transform. Does not have a single root node..”
So in my case i changed my custom xslt to exclude the xml declearation and here we go transform starts to working fine ….
Thank you everyone for your time and thoughts.
Thanks,
Syed Abdullah AKhlaq