A Blessing of Pharasma adds 2 dice to any check where a spell was played. By your own description, on that first check Ezren played Toxic Cloud (by discarding it). This triggers the Blessing of Pharasma to add 2 dice instead of 1.
It doesn't add two dice on any later checks because the spell wasn't played on that second check.
A great way to trigger the bonus die from BoP is by playing a minor spell (like Guidance or Strength) with a different character. The Blessing gives 2 dice as long as any spell is played during that check (doesn't matter who).
