During chapter 3, one of the players tried to use Neutralize Poison. At the time, we got seriously confused by the Counteract rules and just handwaved it as working. Going back now, I'm trying to make sure I'm reading it correctly.
According to Afflictions on page 324, the level of an affliction (poison, etc.) for Counteract purposes is the level of the monster or item causing the affliction. The Counteract level is the level of the spell (3).
So a level 9 enemy poisons someone, and a cleric moves in to try and cast Neutralize Poison on them. We then look at table 9-3 on page 320.
An Ability level of 9 has a Counteract level of 5. Since Neutralize Poison is a 3, you make a check (in this case a spellcasting check, so level+ability mod, or 11 with the characters in chapter 3 assuming an 18 in their casting stat) at a -10 (-5 per Counteract level difference, per page 319). The poison DC was a 23, so they'd need to roll a natural 20 to succeed.
Neutralize Poison can't be heightened, so it's always going to be a Counteract level of 3. It seems like it will quickly become ineffective against equal-level monsters and not particularly effective against lower-level monsters. I'm not seeing any more effective ways of counteracting poisons, either, outside of an Alchemist class feat (which lets you make an antitoxin with a counteract of half your level).
Am I missing something?
I hadn't noticed that, thanks. That helps a bit. In this case, they'd have to have taken Neutralize Poison as a 4th-level spell (of which they only had 2 at 7th level), which would have gotten them a check at -5 instead of -10, so they'd have successfully neutralized the poison in this case on a natural 17+. That still seems like a pretty low chance of success, even if the enemy is +2 levels (high-to-severe threat).
It seems like, if you wanted to be able to counteract multiple status effects, you'd need to consume all your highest level spell slots on things like Neutralize Poison/Remove Disease/Remove Blindness/etc., or get heightened scrolls (or similar) that you need to replace every time you get a new spell level. None of which will be all that effective unless the enemies are at-or-below-level.