Inherent bonuses, in my opinion, are very poorly named. I believe that they simply improve your ability score- just like an increase from levels. However, the game designers thought that it was too easily abusable (since I guess playtester DMs were giving out their PCs hundreds of thousands of GP at higher levels, and/or there were dozens of NPCs more than willing to give up a quarter of their level to increase a PC's ability score) so they called it a "bonus", added a cap, and decided that they don't stack (so if you manage to find a +4 Manual of Gainful Exercise, you're gonna have to cough up 130,000 gp for a +5 in order to get that last +1, or you're gonna have to postpone leveling up and cast Wish 5 times on yourself).
However, aside from all other bonuses, these really don't act like bonuses at all. Inherent Intelligence Bonuses DO increase skill points, for example, and these "bonuses" don't go away in an antimagic field, and can't be dispelled.
It's poor writing if you ask me. Inherent bonuses SHOULD stack, and there shouldn't be a cap. Only a lousy DM would allow it to be unbalanced.