this is an issue which is not really clearly documented and reffers to the Monitor template web application Transaction monitor
Basically if you will want to monitor any SOAP services, this will not work, because at the moment SCOM can only interpret data from REST services.
This happens because SOAP is more freeform then REST therefore the output can be unpredictable.
Also there are no free Management Packs for SOAP web services monitoring. You need to author your own pack using powershell around the COM object 'MSXML2.xmlhttp'. google around for examples.