'Wtf? If they can train new recruits to fly an aircraft or drive a tank or conduct survellance, I'm damn sure they can train them to use a slightly different GUI or a CLI.'
Those are the smart ones, some branches of the armed forces are manned with those uncomfortable with the level of technology available in an anvil. I have on occasion had to explain such simple concepts as 'you don't need to watch the phone in case it rings, you'll hear it'.
For an example of a military specced IT system look at JPA the UK's tri-service administration software. A pig of a system that takes user unfriendliness to a new level while failing in its main job of allowing personnel to manage their own pay and allowances.
A proprietary system is just security by obscurity, it doesn't solve the problem of people taking the easy option like making a print out and losing that, but it does risk the entire defence budget being absorbed coming up with something that's the equivalent of MS-DOS, and not one of the good versions.