Life is not a game - games are life.
1) Blue Darkness Spreads Cards - Saphire's deck in the base game came with a Amarak Peak/Land of the Amazons. In the expansion, this card does not exist. Instead there is a double printing of Blizzard Mountains/Fire River.This change is intentional and explained on the last page of the Dragon Expansion FAQ
2) Black Darkness Spreads Cards - In the base game, there is a Windy Pass/Raven Forest card. This card appears to be missing in the expansion. So Onyx's deck is one card short?There must be a card missing in your copy. My two decks match exactly.
3) Red Darkness Spreads Cards - All of the red cards are one for one except one. In the base game there is a Father Oak Forest/Greenleaf Village card. And in the expansion there is a Serpent Swamp/Greenleaf Village.My base game/expansion Red Darkness Spreads decks have this discrepancy as well; I don't know if this is intentional or not.