I'm going through Book 2 now, and all the encounters seem weak compared to my players. I let them have 20 point buy, but I did the same in Ironfang and Iron Gods and both of those games were lethal af at this same point.
There's a lot more melee encounters through the opening part of book 2. In fact, I think its only really melee encounters, even if you count Jolistina (as she really is just a rogue with some trickster magic) and almost always a party will laugh at a melee encounter unless they are either out of resources and low on hp, or they are just built terribly. But when you get to the end, and you have to fight the entire final dungeon in more or less one go, believe me, the 4 bosses plus one optional boss and 20+ mooks that can all be fought more or less in one or two fights if the party plays it wrong, will put them to a challenge.
Part of it can also be your strategies with it. The vampire spawn encounter can wipe the party extremely easily by dominating one or two of the party as soon as they see them. Vendra can hide amongst the crowd and sneak attack with poison while her guards provide extra flanking. Girrigz is really the only thing that should be a challenge to the party in the sewers, but there is also the otyugh that you can free as a roleplay element to eliminate the majority of everything else there. Fighting underwater in the Direption should throw the party off, as they aren't high enough level for freedom of movement. Jolistina can be a real b*!&* to deal with, especially if the party isn't methodical and is overconfident about dealing with the undead. Lady Andaisin should also know the party is coming (if not all her combat cleric minions as well), meaning she can be fully buffed while the party is still weak after fighting the Leukodaemon.
Another thing to consider as Kasoh already said is that encounter design in 3e was way different than the latter APs of Pathfinder. You can see in book 3 where they give you a three otyughs as an encounter and on top of that you get a NPC who is on par with the party to help, not because it's meant to be a challenge, but just to show how far the PCs have come since they fought their first Otyugh in book 1. These kinds of show off encounters just don't really happen that much in later books, especially after Paizo started really pushing the 15 minute adventuring day design.
I agree, for my group of four players it has been hit and miss. Book three was difficult because of the traps, book four was hard for deaths head vault (almost tpk) and the acropolis. I am in the fifth book right now and they are having a slow grind of it. The saves and energy drain is difficult..I feel the first half of book 6 will be easy for the group but the last half may be tough. All in all, it seems pretty balanced and all depends on how you run it and like the others have said the make up of your group.