File Info may show wrong ink order for a PDF+ file. Calculate Ink Key Settings (CIP3) may create the same wrong ink order for a PDF+ file.
The ink order shown in File Info for a PDF+ may not correspond with the actual ink order of the file (as can be seen in ArtPro+, and in Automation Engine Viewer), for files not containing all 4 process colours.
Also tasks using this info (like the Calculate Ink Key Settings (CIP3) task) may show this in the same wrong ink order in the Document Inks and Separations tabs, and apply it in the output.
Most likely this PDF+ was created by a Convert to PDF+ Action List (in ArtPro+ or Automation Engine) on an ArtPro file or Normalized PDF. PDF+ files created in ArtPro+ usually won't show this behaviour.
This situation is solved in Automation Engine 20.1.
Note you may still see this behaviour in version 20.1, for files that had the File Info opened before version 20.1 (storing the info in a cache file). Remove the .metadata folder (containing the cache), or rewrite the PDF+ (if the file is more recent than the cache, the info will be collected from the file again) to correct this.