In Adobe® Illustrator® a PANTONE ink swatch is duplicated as an unregistered ink and renamed. The LAB/RGB/CMYK values will be the same as the PANTONE swatch, but viewing the normalized PDF in Automation Engine Viewer or when proofing the two colors are different.
When normalizing a file, Automation Engine tries to match up all inks in the file with a corresponding ink in one of the Esko ink books. For example: Automation Engine uses the spectral data from the Esko PANTONE ink book for the PANTONE swatch, while the original LAB/CMYK values from the Adobe® Illustrator® file are used for the unregistered ink swatch (because Automation Engine can't find a matching ink in any of the Esko ink books). The renamed ink is treated as an unregistered ink. This will likely result in a color difference, as the registered ink uses different color data than the unregistered ink.
Register the ink: copy the PANTONE ink from the Esko PANTONE ink book to the designer ink book and rename it to the desired name. This way when the file is normalized the same data can be used for both inks.