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Hello,
There is an incompatibility issue in BHM 4.0 and 4.1 with Feature Pack Update 2 breaking its Maintenance component (not the query/rules repository)
FP2 changed in fact the file version of BTSNTSVCx.exe and the Maintenance component is checking this file to determine the targeted BizTalk version.
This issue is fixed in BHM 4.2 which is now available on the Microsoft DLC : https://www.microsoft.com/en-us/download/details.aspx?id=43716
JP Auconie
BHM team