I just made some pb and choc chip cookies w/my daughter and it seems that no matter how long I bake them they don't get fully done. I added cocoa powder to them, also, and I know if they bake too long they'll be hard and crack b/c of the cocoa and I don't want that, either. I mean, they taste good and look good but should I be concerned that they're not done in the middle? You know, because of the whole egg/salmonella issue? (I ask b/c my young niece was recently hospitalized with salmonella poisoning and now I'm a bit leary of this kind of thing.)

As long as the dough is fully hot, the bacteria are dead. The baking could be a factor of the kind of pan you are using.
Each of these things effect the cookie: An airbake pan slows the cooking.
Is the pan shiny or dark? Are the cookies too thick?

Well, I baked the cookies a little longer and they did get "done" and they became puffy and drier. Even my little girl thought they were from a different batch. They're OK, but I prefer the chewier ones!