In 3.5e, you only receive bonus skill points for your base Intelligence. Extra skill points were gained if you used your +1 ability point / 4 levels to increase your Intelligence score -- however any skill points gained were not retroactive. Magic items and spells that increased Intelligence did not alter skill points -- although Int-based skills gained by the appropriate modifier.
Here are some options I would like to throw out for discussion:
Concern #1: Pathfinder does not indicate if permanent skill gain/loss retroactively increases/decreases available skill points.
My option: permanent skill gain/loss retroactively increases/decreases available skill points. The skill points must be adjusted evenly between existing skills, when possible. (When adjusting for increases, once all existing learnt skill ranks are maxed out, then you can spend points on unlearnt skills).
Concern #2: Pathfinder indicates that magic items have ranks in specific skills built within them. Not only do I dislike this approach, but it reminds me of RPG computer games where you searched around to get items with bonus in all the desired areas (i.e. a chacater may be looking for a +4 Headband of Vast Intelligence that grants +2 Stealth and +2 Perception). When characters buy magic items in town, should I roll randomly as to what skills are attuned to the item?
My option: you do not gain/loose skill points from temporary increases/decreases to Intelligence (i.e.: spells and magic items). All skills checks are modified by the increase/decrease in your Intelligence modifier -- except Intelligence-based skills which are only affected once from the newly changed Intelligence score.
(This is based on the same rational as why Intelligence provides bonus skill ranks. Intelligence is a measure of how well you can perform a certain skill, so a 'sudden significant' gain/loss of Intelligence is experienced in all skills).
This topic has come up before. IIRC, the answer is that PFRPG does give retroactive skill point increases. It's buried in a different part of the book than Chapter 1, but there is wording to indicate this.
And unlike 3.5 (where you gotta keep track of class skills for the purpose of half-ranks and such), once you get those retroactive skill points you can just add them anywhere you want--you don't have to parse out which points were for class X, which were for Y, and which were for Z. Just pick your skills and add the +3 if it's a class skill for any of your classes.
Yes, I can't remember where its specifically spelled out, but yes, your skill points are retroactive when you gain a permanent increase to intelligence. Not only is this a nice benefit for the players, but its a lifesaver for anyone that wants to do an accurate stat block for a character with any kind of intelligence bonus without trying to contort the character so that they "always" had their current intelligence score so that you don't have to do the more complex "up to this level its X" calculations.
I think its been stated on the forums that the reason that intelligence boosting items give a specific bonus to a skill is to keep a character from taking off an item and putting it back on to "retrain" skills as they might want to from day to day.
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I would like a further examination of how far this goes. Do permanent increases to Int grant additional languages known? What about 1st level spells for wizards?
For consistency (i.e., the idea that you don't care whether you started with a given ability score or got it later), I'd like to see the same logic extended across the board, but I'm not sure that's how it's supposed to work.
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Ability Score Bonuses [p388, in the Glossary]
"Ability score increases whose duration is 1 day or less give only temporary bonuses. For every two points of increase to a single ability, apply a +1 bonus to the skills and statistics listed with the relevant ability.
Ability bonuses with a duration greater than 1 day actually increase the relevant ability score after 24 hours. Modify all skills and statistics related to that ability. This might cause you to gain skill points, hit points, and other bonuses. These bonuses should be noted separately in case they are removed."
It seems that ALL statistics are modified; which would indeed include bonus languages and bonus spells. A GM could reasonable argue that it needs to wait until the next opportunity to actually learn a new language or spell, but one could also chalk up instant learning to an epiphany. After all, the character did just get smarter. How often do we actually do that? We learn more, but most of us rarely get much more intelligent. (And in game terms, it potentially happens exactly 5 times in your life.) A sudden jump in intelligence is bound to offer some new insights into things you were exposed to before but didn't totally understand.
This, BTW, was one of those creating-high-level-NPCs fixes, because it was just too hard to calculate skill points and all that when you had to take into account how much Int did the NPC have for the first few levels, then for the mid levels, then at high levels. Now, just calculate back every level with whatever scores he/she has now.