Just as a comparison;
AttributeQueryCommand.xap downloaded from the demo SharePoint site using Site Actions->View All Site Content->ArcGIS Mapping Extensions->AttributeQueryCommand.xap opened in notepad = Length:5446 Lines 34
AttributeQueryCommand downloaded from the demo SharePoint site using the 'Download Sample' function then compiled by my VSE 2012 produces AttributeQueryCommand.xap when opened in notepad = Length:5269 Lines 43
??
Cheers, Peter