Processing a JPG and the same image as a PDF with the same settings with the same PrintEnvironment (incl. output calibration) leads to different colors on the printout.
This might happen when the images have a profile assigned but should get replaced by another ICC ("Ignore embedded").

Please note, we recommend using the embedded profile. Nevertheless, there is a solution for this very rare situation.

JPG files are pixel-based and can get dithered without an intermediate step. PDF files need to get flattened and rasterized before being dithered. Because a PDF can consist of different elements with different color spaces, the rasterization process contains a color management part. Happily, Ergosoft provides a variety of PDF interpreters. Depending on the input file one or the other PDF interpreter matches the colors better to the JPG.