But isn't the data from those boxes being transmitted to the ground in real time?
The OI [Orbiter Instrumentation] data is combined with a number of channels of digital voice data in a black box called the NSP [Network Signal Processor]. From there it goes to the OPS recorders, and the S-band system for transmission to the TDRSS satellites, then to the ground.
It can also go directly to the ground, but that wouldn't work since they were in the "re-entry ionization blackout" at the time, and they have to be over a ground station anyway.
The engineering data (strain gages and thermcouples, etc.) are recorded on the OEX recorder for retrieval only after landing. That data is not downlinked.