This occurs because [Composite Overprint] is not set to ON.
*Composite Overprint: Prints the colors of objects overlaid across composite layers as is. The colors of those sections in which multiple layers are overlaid become mixed during printing.
Turning this setting off means that the colors of the lower layers do not affect the colors of the upper layers, and therefore, for overlaid sections, only the color of the top layer is printed.
15 minutes or less
Set the [Composite Overprint] setting to ON.
Setting this to ON may cause the RIP processing speed to drop.
The procedure detailed below uses PS Plug-in Driver.
1. Open the PDF, select PS Plug-in Driver, and open [Printing Preference].
2. Select the [Color Management] tab, and click [Get Color Management Data].
3. Add a check to [Use Manual Settings], and select [High Quality] for [Composite Overprint] in the [Optional Settings] tab.