Strange cuts when flattening transparency

Hi All,
how can I avoid these cuts when flattening transparency in illustrator?
I'm preparing artowork for print. This specific banner is a real size so they won't enlarge it but I have gotten feedback before that these lines appear on the print.
Previously they dindn't appear so I thought its a glitch in the pdf viewer
I think they come from these shapes that illustrator cuts the shadows and shapes into

What am I doing wrong?
I have different layers a tif background, some opacity gradients on top of that and other solid shapes with drop shadow.
Is there another way of expanding these and flattening than selecting them all and flatten image and keep transparency?
If I do each layer one by one then the visuals change a lot the images become dull and shadows change in appearance.


Thanks for the help in advance!
