LAYERNOTIFY is set to 1
LAYEREVAL is set to 1
LAYEREVALCTL is set to 15
Just to make sure I wasn't going crazy I created 2 new drawings with xrefs. I created a new sheet set and imported a layout from each of the new drawings and a layout from an old drawing. I closed all the drawings and made a new layer in one of the xrefs. (FYI: All the layers in the 2 new drawings were unreconciled). I then published the sheets from the sheet set manager using the "Publish Dialog Box..." option. I published to DWF and used the Publish in Backround option.
Everything published fine.