There is the issue of the behavior of the mapping process creates invalid XML.
The input instance looks like this:
<xml>
<loopA />
<loopB />
<loopA />
<loopB />
</xml>
However, when using the mapper, you create your output and it ends up looking like this:
<xml>
<loopA />
<loopA />
<loopB />
<loopB />
</xml>
How to get this to work (only in R2) is to open up the btm file and change the following attribute from its default value of No to Yes in the mapsource element
PreserveSequenceOrder="No"
<mapsource Name="BizTalk Map" BizTalkServerMapperTool_Version="2.0" Version="2" XRange="100" YRange="420" OmitXmlDeclaration="Yes" TreatElementsAsRecords="No" OptimizeValueMapping="No" GenerateDefaultFixedNodes="Yes" PreserveSequenceOrder="No" CopyPIs="No" method="xml" xmlVersion="1.0" IgnoreNamespacesForLinks="Yes">
Here is the new code:
<mapsource Name="BizTalk Map" BizTalkServerMapperTool_Version="2.0" Version="2" XRange="100" YRange="420" OmitXmlDeclaration="Yes" TreatElementsAsRecords="No" OptimizeValueMapping="No" GenerateDefaultFixedNodes="Yes" PreserveSequenceOrder="Yes" CopyPIs="No" method="xml" xmlVersion="1.0" IgnoreNamespacesForLinks="Yes">