Remove the 2 DTS packages: EDIReportingActivityDefs & AS2ReportingActivityDefs from the bm.exe command line which do not get automatically removed when you un-install the previous version:

C:\Program Files\Microsoft BizTalk Server 2009\Tracking>bm.exe remove-all -DefinitionFile:"C:\Program Files\Microsoft BizTalk Server 2009\EDIReportingActivityDefs.xml"

C:\Program Files\Microsoft BizTalk Server 2009\Tracking>bm.exe remove-all -DefinitionFile:"C:\Program Files\Microsoft BizTalk Server 2009\AS2ReportingActivityDefs.xml"