This bug is going to affect everyone so we need to announce it here. It turns out we have not been calculating the military score correctly. Thanks to Admiral Thrain and ChallengeSpaceyard for discovering this.
What has been happening is that Engines, Torpedo Launchers and Beam weapons have been added to the score value of your ships only once. So even if you have 2 Transwarp Drives, 10 Beams and 6 Torpedo launchers (like a Victorious) your actual score value would be as if you only had one engine, one beam and one Launcher. This unfortunately has a huge affect on the score when you have a lot of ships.
While I wish we had found this bug sooner, we did not. We must correct it. The fix has been put in place today and will affect the score in your game on your next host run. Expect to see big swings and shifts in score as the "real" score shows itself.
This is a good example of why we're still in Beta... thanks for your understanding!