Properties have been known to mis-code stays when they don't understand the rules. There have been posts about credit being denied when using a card with the word "Corporate" on it and even when a spouse used their CC and not a card with the guest's name on it.

Company billings typically come in two flavors, Direct Bill and Master Bill (at least SPG distinguishes between the two). Direct Bill being when specific arrangements are made for individual travelers and the room is billed separately. Master Bill is when a group of people (maybe a conference) are being covered and a single bill is submitted for all rooms.

You should get credit for Direct Billings. The thought being the individual may have had some say with Direct Billings but not Master Billings. You should talk with your travel department to find out what they negotiated with the hotel and make sure they are in compliance. It is possible for them to have secured a lower rate in lieu of giving any program credit. After all, they do cost the property something.

Otherwise, you should contact MR and ask them to investigate. Keep in mind the first response may be in support of the property and you will need to push back (at least that is what has happened to me).