Applied online and heard back from HR about a week or so later. Scheduled a phone interview about a week after that. Phone interview had 3 parts: 1) Quick talk with security person, I already have a clearance so she just asked for my info so she could look me up and verify it 2) Technical interview with 3 hiring managers 3) Chat with HR about company, benefits, and any further questions. Phone interview took a little less than two hours. An offer was made to me approximately two weeks later.
All was well and I was very interested in the company and overall pleased with the offer. I tried to negotiate $5k more in salary and HR replied that it would be "very difficult to get that" so I responded citing two sources (LinkedIn and a government contractor wage survey, both local to San Antonio, not national averages) that there offer was $10k under the average for an EW Engineer in San Antonio. They interpreted this as me being unhappy with the offer and that I would be unwilling to stay with the company and they rescinded the offer three days after making it (and after I had already signed and accepted it with me explicitly stating that I was not unhappy with it, merely trying to negotiate and get the best offer possible).
They apparently have a problem with people using them to get a clearance then going somewhere else for better pay. In my opinion they need to reconsider their salary offers. Their offers are clearly not competitive and management is extremely paranoid about people being unhappy with the offer and not staying at the company.
I must give credit to their HR representative. He was very personable and easy to deal with and very understanding of my explanation but it was management's decision and they made up their mind. Reading other reviews here it seems management is clearly a problem at this company. Guess I dodged a bullet.