RS mentioned the reason why. If you only have 1 crystal in your possession, then you only bring in 1 point a turn. If you have 2 crystals in your possession, then you bring in 2 points a turn, etc etc.
Lets look at the numbers then. You caught the Drath on turn 2 of owning any crystals. They only held 1. So:
Turn 1: 1 crystal, 999 turns to go (1 point earned)
Turn 2: 1 crystal, 998 turns to go (2 points earned)
Turn 3: 2 crystals, 498 turns to go (4 points earned)
996 crystals to go, gaining 2 a turn means in 498 turns at this rate they will hit 1,000 earned.
The countdown doesn't show number of crystals needed, it only shows number of turns remaining at the current rate. Since the current rate doubled, thus the countdown clock got cut in half.
