The way I see this:
Permanent Bonuses: Ability bonuses with a duration greater than 1 day actually increase the relevant ability score after 24 hours. Modify all skills and statistics as appropriate. This might cause you to gain skill points, hit points, and other bonuses. These bonuses should be noted separately in case they are removed.
Say you wizard started out with a 17 INT .. and at 4th-lvl gained the ability increase +1 to INT and you have an 18 INT.
I see it like this: you went from a +3 bonus on all INT Skills to a +4 bonus (hence increasing skill ranks retroactively.) Also, at 4th-lvl you get the +4 now to the Class 2 skill points to equal +6 skill ranks instead of having only the +5 with the 17 INT.
That's how I've always saw that. Not gaining an additional skill rank for 1st - 3rd levels "retroactively".
For me this also works for bonus languages you get .. again 17 INT at start of game getting 3 languages plus racial ..
Now at 4th-lvl you gained an 18 INT granting an additional language you can learn. (it should not be instantaneous, it should be learned during the course of play IMHO).