Clip takes the VIN from ECU so with your old immo data, it will recognize ECU and clocks, because they fit Clip database for a Megane. When the ECU is virginized, Clip tries to obtain VIN from other modules, so the ECU is not recognized as it doesn't fit the database entry of your Kangoo (I assume it wasn't S3000 ECU originally).
You can try to modify Clip database, but I think writing VIN with DDT4ALL or Pyren will be much easier, as they are not as fussy about compliance with VIN database.
One thing you can try with Clip, manually enter this VIN when connecting: VF1FW0WC541266230
When I was playing with immo and no engine installed, i disconnected fuel pump and wired blinker bulb in place of starter and it worked fine.