BizTalk Trasforms only one XML properly

We are working on BizTalk project; we have implemented all steps in orchestration and are working as per the requirement except following issue:
Transform shape transforms two source schemas and to one destination schema. After transformation noticed that it transforms data of one XML properly but it is not transforming the data of other XML.
Details are given below:

– Input schema contains data as elements. Generates the XML using SQL adaptor, XML contains only one record.

– Another input schema contains data as an attributes. XML is generated through the code and XML contains many records.

– Output schema contains data as an attributes. The generated XML is result of above two XML which is having data element as an attributes.
The issue is in the Transformation it transforms the data from XML which having data as an element form and for other XML it is not transforming the data which is having data as an attribute form.

Any clues why?