Yes, it’s been known to happen and I’ve been warning people about it for some time. In your case, what I would do is point them to the approved apps that are similar to the rejected one and hope for the best.
What was the application you submitted and was rejected? What kind of interactivity did you use? And did you mention it was a book when submitting it? Check out this thread for some tips on smoothing the approval process: http://forums.adobe.com/message/4490206#4490206.