If it is a read & play book, for example, Go Dog Go, it is ONLY available on the Nook Color. I also have an iPad2 and can't get any of these books on it. It is because the read & play books require Flash, which the iPad & iPad2 does NOT support. If you look at the book, it will tell you if it is available for only the NookColor or if it supports the iPad application. So far, I have been able to open all books on the iPad application except for the few read & play books that are available. The read to me books are fine to open on the iPad app.
Hope this helps, Michelle