The official Pokémon TCG Online website has revealed that starting in the new set Black & White—Plasma Storm which was released on February 6th, 2013, unlock codes in physical booster packs will only unlock cards from that set in the digital version of the game. Below are the full details.

Changes Coming to Pokémon TCG Online Code Redemptions!

Starting with the Pokémon Trading Card Game: Black & White series, specially marked booster packs have included a Pokémon TCG Online code card. These codes can be redeemed for booster credits in the Pokémon TCG Online shop, which can then be used to unlock digital booster packs from any expansion available in the online game.

During the early stages of beta testing, the booster credit method provided access to expansions that were in the online game but did not contain code cards: the HeartGold & SoulSilver series and the Call of Legends expansion. While complex, the booster credit system created a diverse card pool, allowing players to construct a wide array of exciting decks.

Now in its second year, the Pokémon TCG Online has 12 expansions available, with number 13 coming in February 2013: Black & White—Plasma Storm. As the card pool continues to deepen, the need for this complex booster credit system has decreased. Over the next 18 months, a more streamlined redemption process will be rolled out, making it easier than ever to get straight into the game.

Beginning with the Black & White—Plasma Storm expansion, each Pokémon TCG Online code card found in a booster pack will unlock a digital booster pack from the same expansion, rather than a booster credit. For now, code cards from earlier expansions will continue to unlock booster credits, which can be redeemed for any expansion released before Black & White—Plasma Storm that is currently available in the online game. When the transition is complete, unredeemed code cards from every Pokémon TCG expansion will unlock digital booster packs from the same expansion. Booster packs from expansions that do not contain code cards but are available in the online game will be available by other means.

Our goal is to complete this transition before the end of 2014. We will continue to keep the community informed via news articles as the transition progresses. Each article will outline the next step in the process and will be posted a minimum of 30 days before that next step goes into effect so these changes do not catch players by surprise.

Source: http://www.pokemontcg.com/news/?p=315