After 72 hours before departure, any changes to the secure flight data causes and immediate resending of the data for TSA to review. Many examples of this being instantaneous on FT.
I highly doubt this has anything to so with FF number not being passed through. Corporate travel agent never sent the KTN which is problem.
In the example by FlyAO2, when you log in to your skymiles profile when you book it auto populates KTN and FF number and secure flight data in the reservation.
When you book through a third party, you are relying on them to supply all the data. Its not auto populated based based off your skymiles profile.
The following is an example of the
only time person did not get pre, happened to be the day they had no control over the booking process and was relying in airport agent to properly fill in the secure flight data
http://www.flyertalk.com/forum/23355005-post10.html