One of the controls available in your Nightly Configuration is whether potential selections should be checked for exclusion by Series.
What you may not realize is that isn't just looking at whether the patron has an exclusion against that series. It also looks to see whether they have a preference--so it doesn't send a book ahead of sequence.
For example, say that your patron has preferences both for James Patterson and for his Alex Cross series. If your Nightly Author program has the Series check activated, it will look for James Patterson books to send to her... but it'll reject any it finds from the Alex Cross series, leaving them to be sent in order by the Series preference.
This is just one example of how complex Nightly is, and how many levers are available to you to set up to work just right for your library. If you have questions about the Series check, or any of your other Nightly Configuration settings, let us know!