Thank you so much! I did use the bulk metadata edit to set most of my collection series, but I could have sworn I set the series index as well. Usually I do it as "Series Universe " and then continue through to the next chunk of books that need "Series Universe [#]" until I get them all.
I did fix all the ones that showed up with the search string you gave me and they're all showing up correctly on my nook, now. Thank you again!