Paizo have published a revised rulebook, and the game designer has posted a sticky in their forum clarifying a lot of the rules:

Some Thoughts After 1500+ Pathfinder ACG Threads       

Here are the links to the revised rules and FAQ:

Pathfinder Adventure Card Game Rulebook

Pathfinder Adventure Card Game FAQ

And here is the content of the designer’s rules sticky posting (which are also included at the end of the new revised rulebook):

1. The cards do what they say.
1A. If a card doesn’t tell you it does something, it doesn’t.
1B. If a card doesn’t say when it does something, it can do it any time cards can be played.
This sweeping rule tells you to read any card as it is encountered or played, and do whatever it says as soon as possible. You don’t look at the rulebook first; you read the card and let it tell you what to do. Examples: A character can play an armor regardless of whether she has armor cards in her deck list. A spell may be cast any time, except during times when cardplay is expressly prohibited. A weapon cannot be used to acquire another weapon because it only says it assists with combat checks. A monster that’s immune to Mental traits cannot be evaded by a Sleep spell. “After the encounter” damage occurs whether or not you defeat the bane. You can’t roll a recharge check for a card that says “Recharge: None.” Any number of players may play blessings at once, from anywhere. If a card doesn’t say it works on “your check” or “another character’s check,” it works on anyone’s; if it doesn’t say where it works, it affects a character at any location. And so on.

2. However, cards only work when it’s appropriate that they work.
Cards’ powers only relate to the specific situations they reference, and if you’re not in those situations, you can’t play them. You don’t ever try to acquire the card you flip off the blessings discard pile, or one that’s already in your hand. If you examine a card, you don’t have to encounter it unless whatever let you examine it requires you to do so. You can’t cast Cure in response to taking damage, because Cure isn’t about taking damage. You can’t play Detect Evil on a location that has no cards. Valeros can’t recharge a weapon if he discards it as a cost to trigger another card’s effect, because he’s not playing the weapon for its effect, just as payment for the other card to work. Nothing works unless it makes sense.

3. It’s your encounter, and no one else can resolve it for you.
Whenever you encounter a card, or make a check, you – and only you – must resolve it. No other character can evade it, defeat it, acquire it, close it, decide what to do with it, or fail at doing any of those things. If Sajan encounters a monster, Merisiel cannot evade it for him. If Harsk encounters a card, Seoni cannot defeat or acquire it for him, unless it requires two checks to do so, in which case Harsk must attempt at least one of them. If Ezren defeats a henchman at the Sandpoint Cathedral, Seelah cannot discard a blessing to close the location. In other words, if you need to wait your turn, wait your turn.

4. Cards don’t have memories.
You may have to remember things to play this game, but your cards don’t. They forget they’ve been played after they’ve done whatever it is they do. So if you reveal a weapon on a combat check, and then have to make another combat check in the same encounter, you can reveal that weapon again. If Kyra discards a Cure to heal herself, and then a card puts that Cure back in her hand, she can use Cure to heal herself again. Displayed cards work as long as they’re displayed. This rule doesn’t mean that things you did earlier in a check don’t matter, though; you still need to know whether you played a 2-Handed weapon when you try to play your Wooden Shield, for example.

5. Everything that happens inside a step is part of that step.
There are discrete steps in a turn: advance the blessings deck, give a card, move, explore, try to close a location, reset your hand, end your turn. When you encounter a card, you can evade it, apply any “before the encounter” effect, attempt its check, do any additional check, apply any “after the encounter” effect, and resolve the encounter. Each of these steps is an opportunity to play cards, and the rule about playing one card of each type applies to each such step. Also, damage can occur on a lot of those, and when it does, it’s still part of that step. So if you played an item to increase your roll on a check, you can’t use another item (or even the same one) to reduce damage. It’s still in the same step.

6. There are no nested checks.
A check must resolve entirely before another check can be initiated. For example, for a villain with two combat checks, you must finish the first one before starting the second. If different players can temporarily close several locations, they must resolve them in an order of their choice. If a spell or other card used in a check is available for a recharge check, put it to the side where it is not available for taking damage or any other purpose, and then when you’re done with the first check, make the recharge check. Checks and damage dealings that occur “before the encounter,” “during the encounter,” and “after the encounter” are different checks and damage dealings, and you can start the 1-per-card-type over at each one. If two checks can happen at the same time, the player whose turn it is determines the order of the checks.

7. Skills and dice are not the same.
This game frequently asks you to roll a “Strength check” or a “Perception check.” That’s a simple concept that has some complexity to it. When you have a skill, you roll that skill’s die plus any bonuses listed by that skill; if you don’t have the skill, you roll a d4. But when a card gives you another die of that skill (the same size as you get from the skill), that’s all it gives you. You don’t get your bonuses again. You don’t get the skill associated with that die. You don’t get the ability to recharge a spell that requires the Arcane skill if you don’t have it. You don’t get the ability to play a Blessing of Gorum for 2 dice on your Longbow, because you’re not making a Strength check. You just get a die.

8. Boons that let you make checks give their traits to those checks.
If a card you play tells you how or when to make a check to acquire or defeat – and only in that case – apply that card’s traits to the check. Ranged weapons give the Ranged trait. Magic weapons give the Magic trait. Divine spells that let you use Divine as your combat check give the Divine trait. For example, Lightning Touch tells you to make an Arcane + 2d4 combat check, and thus it applies Magic, Arcane, Attack, Electricity, and Basic traits to the check. Guidance, on the other hand, does not tell you to make a check, so it does not apply any of its traits to the check, regardless of the fact that it is only used in checks.