Hi there, I know this is a little late, but I have just run into this problem myself and believe I may have the solution for you. I had elements on my pages with a drop shadow applied to them individually, and got the slight change in color as you did. Here is what I did to solve the problem:
Instead of making them all separate, group the elements on each page you want a shadowed into one group by selecting them and pressing CTRL + G or APPLE +g for mac. Then draw a blank transparent rectangle around the entire page on a separate layer making sure it exceeds the bounds of the page. This is done to keep the colors consistent. I like to put the rectangle on a separate layer so I can turn it on and off with layer visibility in order to select the elements below it.
After that is done, select the previous group you made and group it with the new blank rectangle. Then apply the drop shadow to this new group.
Now when you export you pages to pdf, the boxed screening around the elements with shadows should be taken care of. Hope this helps.