Why do non-flattened PDFs display incorrectly on PCs?

We have found that PDFs do not display correctly in Windows if they were generated from InDesign files with transparency layers on a Mac. They look fine in both Acrobat and Preview on the Mac, but not on Acrobat for Windows. This problem shows up in multiple versions of Windows and Acrobat for Windows.
I understand how to resolve the problem by adjusting the flattening of transparent objects, but I want to more fully understand why it happens.
1) Why can't Windows display PDFs with transparent objects without flattening them first?
2) When generating PDFs from InDesign, is there a preferred method for avoiding this problem in the first place?
3) On several occasions, print shops have had trouble with these same PDFs -- some element is missing, but not necessarily what was missing on the Windows computer. Is this also related to transparent objects?
Where can I, as a IT professional, learn more about this? It seems like this is a fairly widespread problem, but I'm having trouble really understanding what's going on.
Thanks for your help!
Eric

Thanks for your reply. I may have exaggerated by saying "widespread," but it's a problem in our agency as well as at least 7 other clients I do technical consulting for.
Not being a designer myself, I'm not sure what information would be useful. I'll ask one of our designers to create a document that exhibits these problems and upload it. Would that be helpful?

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<</Filter [ /FlateDecode ] /Length 120>>
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