Probably ...Nothing to do with reservations made using the large well known official corporate booking agencies/tools fora room using companies corporate rate. It is the deal your company makes with MR/HH/IHG/Hyatt that will determine if points earning as Companies can (and some do) negotiate for slightly lower rate by excluding chain/hotel room earning points.

If you look at terms of that rate in your booking, you'll see these corporate rates are "non comissionable" , so the travel partner making your booking booking earns nothing. The chains MR/HH/IHG etc don't exclude these bookings.

Typically such agency in lieu of comission relies on that your company then is instead contracted to pay both yearly service fee and pay additional usage fee at end of each quarter/year to your corp travel agency based on volume of bookings made for rooms+flights.

Thus at end of day, if booking corp rate via official company booking channel (ie agency like Amex, CWT) your rate is qualifying, points earning unless your company negotiated away that part in return for lower nightly rate.

Also possibly, if your company lacks negotiated corp rate, requires you book through 3rd party that in turn claims commission on each room booked, such booked reservations are standard adr/flex and comissionable, I can see how you end up with non-qual nights without points. It is bookings through 3rd party channels funded by MR/HH/IHG paying comission (rather than company paying annual fees) that are non-qual stays.