I've never had an issue with associating business bookings made through company travel portals, like Concur or AmexTravel, to any rewards program. In fact, both of them will prompt you for the rewards number when booking online or calling over the phone. Also, never had any issues calling Hilton customer service line asking them to associate a reservation booked through company to my rewards account, though I usually do this right away after booking and days ahead of the stay. However, I can definitely see the possibility of a hotel denying you benefits if you wait until check-in as it is at the hotel's discretion.