Transparency is missing from .ai files

I (InDesign) have recently lost the ability to be able to see through where the transparent aspects of an .ai file are through to other layers and objects in ID CS5. I've created many files and used existing files where I know that there are transparent areas (and even tested them on other computers) and on mine, I cannot see through where there are transparent areas, but they show up fine on other computers (can see through).
I've looked through all my preferences and other panels and haven't been able to figure out what is going on. The transparency works fine when I save the .ai file as an .eps (Illustrator).

...be sure to show options and select transparent background.
^Right. And, I can't be sure about earlier versions, but in CS6, I've noticed that the setting is now "sticky." At some point I deselected Transparent Background, and then when I placed without Show Options, selected, I got non-transparent results. It will stay on whatever you set last until you set it otherwise.

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Transparency is missing from .ai files

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