It's quite likely that you company travel agent booked it through a provider that doesn't earn points/nights. It's *always* been a policy that only rates booked through direct Marriott channels (including most regular travel agents) are eligible. Rates booked through OTAs and sites like booking, kayak, hotels... will not be eligible. There have been reports on Flytertalk of company travel agents messing up and using an aggregator.

BTW, if it turns out it's not Marriott's error, and it is, in fact, due to how your agent booked, are you going to stick with Marriott and change your username, or will you throw 17 years of loyalty relationship down the drain over one unrecognized booking?