I thought this was an interesting story, but before anyone leaps to conclusions -

"More likely, the TSEC equipment is the encryption box routinely used to receive messages from Mission Control in Houston. NASA codes its messages to the shuttle so no one can intercept them and play them back later to the shuttle, fouling its flight control. "

Our spacecraft have flown with some kind of encryption technology since Gemini, IIRC.

HoustonChronicle.com - Top secret part among the shuttle debris