There is a known issue regarding the behavior of imported graphics when exporting to PDF or Printing on Windows devices.
When a graphic is imported into a Finale document, it's positioning from the score is also copied onto any linked-parts. Either repositioning or hiding the graphic in the parts will unlink it from the score, allowing for the same graphic to have multiple independent positions in a document.
Graphic positioning before exporting both the score and parts to PDF
However, exporting to PDF or printing multiple parts at the same time will result in the first part's graphic positioning taking priority over any subsequent items.
Graphic positioning after exporting both the score and parts to PDF at the same time
To maintain independent graphic positions when printing or exporting to PDF, you will need to print each part one at a time. In other words, instead of a single print job with both the score and parts, you will need separate print jobs for each item to maintain independent positioning.