Does the same rule apply if an itinerary contains different airlines?

For example MAN-LHR-MSP-LHR-MAN with the MAN-LHR-MAN sectors on BA and the LHR-MSP-LHR sectors on Northwest.

The corporate travel agent booked me the above itinerary instead of just LHR-MSP-LHR. They stupidly copied my colleagues itinerary which is from MAN!

I only spotted the yesterday and the corporate travel agent says that it's all fixed but the Northwest website and their call centre tell me that my itinerary starts in MAN.

I contacted the corporate travel agent again today and they just say don't worry! Unfortunately the NWA system says different!