Illustrator CC 2014: Save As PDF, Flatten Transparency Issues

Hi All,
We created a PDF presentation that's about 40 pages in Illustrator and had some display issues with previews in Box.  Upon inspecting the bug, we realized that Box's preview function does not display transparency properly (or at least seems to have issue displaying transparency if it hasn't been flattened.)  We tried flattening the transparency of our Illustrator file, but when we do this the PDF has faint box outlines around objects. 
Can anyone recommend a solution to this issue?
Thanks!
P.S.  I'm new to figuring out which PDF Presets to use to optimize my presentation for desktop/iphone/ipad presentation.  Right now we are using Press Quality with Preserve Illustrator Editing Capabilities unchecked and Optimized for Fast Web View. 
P.P.S. We tried Acrobat 5-8 Compatibility for Box, non worked.  Acrobat 4 with flattened transparency displayed properly, but had the problematic outlines. 

Anyone have any input?
Thanks!

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