Guys read this!
The pdfs and books are there in the phone, and by phone i mean iPhone 3G without the S.
But the problem is, the iPhone 3G simply does not have the hardware to support the full functionality of iBooks. therefore, what most of you are experiencing is, simply put, the extreme lagginess of the phone. the phone is too slow to show all the books, for example, the guy with over 100 books. books are loaded before pdfs are loaded, therefore if you are able to see the books you will have to wait another maybe 5 mins to see the pdfs? that was what happened to me, i left the phone alone for 5 mins and everything showed up, but extremely slowly.
Conclusion: iBooks works like a snail on iPhone 3G, but for the faster iPhone 3GS or the iPad, such a problem should not exist, unless you have hundreds of books
Hope it helps!