The contest is made up of multiple categories. Each category is worth one point toward the total score; the percentage of the total points held by your team is the percentage of one point your team has for that category.
Categories are in the form of multiple puzzles: for each puzzle presented, a case-sensitive answer must be found to receive the amount of points that puzzle is worth. Any team may answer any puzzle question at any time. A new puzzle is revealed when a team correctly answers the highest-valued puzzle in that category.
Many Capture The Flag contests attempt to reward teams who answer quickly, by adding a "quick answer" bonus or by decaying point values over time. Our contest doesn't work this way.
We want to focus on rewarding technical proficiency, allowing skilled contestants to prove their worth independent of their ability to hit F5 quickly. It is our hope that by providing enough things to work on, quick-moving teams will emerge with more points by solving lots of puzzles, while novice teams get a solid benchmark against which to judge their technical skill level: you don't have to make allowances for reaction time in comparing scores. In addition, when the game infrastructure goes down—which seems to happen a lot in anybody's CTF—there's no losing points while the organizers struggle to get things back up.