I'm unconvinced that the security alert is due to the Shuttle, merely pointing out a possibility.
For instance, the backup plan for the Shuttle (if damaged during launch, say by falling insulation) is to dock at the ISS, leave the crew there, and bring the Space Shuttle down by remote control, unmanned, via one or more of our Space Command sites.
Those Space Command sites are on heightened alert 12 hours before the Shuttle Launch...thus, a possibility (i.e. don't want some sort of bad-guy controlling where the Shuttle lands under remote-control).
Then I'd think the NM alternate landing site would also be on alert.
I know bases here are very tight. No entering the bases unless your name is on the list. It has to do with the 4th, and some VERY IMPORTANT people coming here.