There's a difference between an online travel agency (I use the acronym OLTA instead of OTA, since for me OTA means On-Time Arrival) such as expedia, orbitz, priceline, etc. -- and an honest to goodness old-fashioned travel agency such as what many corporations still use. The former does not qualify for points; the latter does. But with the former, YMMV. You should be able to pick up that reservation online entering your IHG confirmation number and last name, and adding your IHG Rewards.
Also try modifying the reservation.
Note that even if your booking doesn't qualify for points (and promos such as Accelerate), you should still qualify for most of the perks of your status -- welcome amenity, upgrade, etc. If Royal Ambassador, you'd likely still have the Club access and the free minibar even if you don't qualify for points.

Personally if I'm not sure a reservation made will qualify, and it's not prepaid, I would try to make another reservation on IHG.com and cancel the original reservation -- unless the original reservation is at a lower rate. I'd also trigger Ebates to get the 4.5% or more rebate.