Welcome to Flyertalk McLovin' (and cool username)
It sounds like something isn't right here. I regularly book Hilton properties through my company's booking engine (per company standards), and I've never had an issue getting points. Within 5-10 min of booking, the stay shows up on the HHonors website, and stay/points credit shows up just like any other stay/points credit. I also work for a large company, and the rate can be significantly lower than through the HHonors website.
Definitely call back, or even send an email (and a copy to the Flyertalk rep may not hurt).