OP - How are your rooms billed (other than incidentals)? Do you pay for the room with a CC or is the room itself billed back to your employer in one form or another?

It is also possible that your employer or an agent for your employer, has negotiated a discount with Marriott which does not include points. Your employer gets a better rate for that.

But, the real bottom line question to you is what did Marriott say when you called to ask why the rate is not qualifying. Until you get a clear answer, it is hard to advise what the next steps, if any exist, might be.