I'm a Govtrip user as well (the "E-Gov Travel Center for Excellence" just emailed me to tell me everything is just fine, so it must be back) and my primary question is why do we have defense contractors running internet travel sites?
Govtrip took a long time to become ready for prime-time and to this day isn't a model of the programming arts.
Wonder how much it costs...
A greater concern is "Electronic Questionnaires for Investigations Processing (e-QIP)". If you need a security clearance you go to the e-QIP site and put in your life history, friends, bank info, credit history, medical history, everything.
It's a identity thief's dream, absolutely everything needed for somebody else to become you. In fact someone with this kind of information would have a better claim to being you than YOU would.
But don't worry, it's hacker proof.