Are you using any spot colors, because that sounds like an issue that spot colors can produce as there is no transparency with spot colors even though on screen you can see it?
You can save the file to .pdf and see if it prints correctly that way.
You can also merge your layers to a 300 dpi or higher bitmap and print from the bitmap, you will have a crisp image because the dpi is high enough. But save your vector file with another name because you will lose your vectors after merging to bitmap.
Every day's a new day, "draw" on what you've learned.
Sally M. Bode
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