Given how quickly things change in a playtest, I figured I might as well start a new thread. Apologies if that's inappropriate.
The title above represents what I think is the most tricky part of adjudicating afflictions. Pertinent are the following:
"If you have a persistent damage condition, you take the damage at this point. You also attempt any saves for your afflictions at this time." (End Your Turn, Playtest Rules, p. 306)
"When you're first exposed to the affliction, you must attempt a saving throw against it. . . If you fail the initial saving throw, after its onset period (if applicable), you go to stage 1 of the affliction and are subjected to the listed effect. On a critical failure, after its onset period (if applicable) you go to stage 2 of the affliction and take that effect instead." (Afflictions, p. 325)
So your hapless PC is bitten by a giant centipede and fails a saving throw. Centipede poison, Stage 1, causes d6 damage and flat-footed for one round. Does this begin immediately, as the Afflictions quote states, or at the end of the player's turn, as the End Your Turn quote indicates? I'm inclined to think it's immediate, under Specific Overrides General. If so, though, when does the poison's effect roll over? One round of flat-footed would end on the centipede's next initiative, and repeat saving throws to resist the poison occur at the end of the player's turn.
The closest I have come to working this out is to have the first effect of the poison begin immediately, then take the interval between the centipede's action and the end of the PC's next turn to be the first round of the poison's duration.
Another way I've seen suggested is that the PC makes an initial save immediately, but starts the effects of Stage 1 at the end of the PC's next turn, thus getting the durations to even out. On a failure, PC takes d6 damage at end of turn and becomes flat-footed until the end of the turn after, at which point a second saving throw is necessary. This would be the same, essentially, as delaying the initial save until the end of the character's first turn post-bite.
How does this play out at your table? Whatever the answer, I would love to see a round-by-round example included in the Second Edition rules to avoid confusion. I also might suggest that repeat poisonings reset the maximum duration.
Persistent damage is different from afflictions. At first glance, they seem the same but mechanically they are quite different:
With persistent damage, you are literally on fire or being dissolved in acid or in some other way taking constant persistent damage to your Hit Points. Whatever this persistent damage is, there is never any onset period (when you get set on fire, you begin burning and taking damage within the same round). You take the same amount of damage every round at the end of your turn, then you get a flat check to end the persistent damage. It's not a saving throw, it's a flat check.
With afflictions, you might not be taking any damage at all, though most of them do some small amount of damage. There is an onset which could be a fairly long time or could be no onset at all (zero time, immediate effect). You don't suffer the affliction at the end of your turn; it affects you immediately when the onset period (if any) is passed (for example, being stung by a scorpion causes you to get immediately poisoned - roll the save right now and apply the poison effects right now if you fail the save). There is no flat check but you do get a saving throw of whatever type is appropriate (usually FORT but not always). You might need more than one successful saving throw to end the effects. Failed saves usually make the affliction get worse (cause more damage and/or stronger effects) while successful saving throws usually make the affliction get weaker (less damage and weaker effects).