Varying black intensity in PDF/InDesign preview - any ideas if harmful?

Hi guys,
I am encountering the following oddity in displaying my book as PDF or even inside Indesign.
The intensity of my Black color is varying on some spreads pretty randomly. Look at the picture below to see what I mean. Notice the difference between the upper and lower part on the left.
You see, how to the upper part is less black? Of course, since this is a threaded text, the text is exactly the same attribute-wise. There are also no overlaying or overprinting features on top, bottom or whatsoever. Black text on white paper.
Anyway. So I thought: This looks weird. I checked the color values in Photoshop by importing and rasterizing the respective pages. They seem to match. I did a print test, they seem to match.
Now the funny part: I thought, this must be an anti-aliasing issue so I made a screenshot from Acrobat and Indesign and what I see is that the text on the pages get anti aliased differently! (right column)
My question now is:
Why?
Where do I set it up to be the same?
Does it have effects on printing?
Thanks a lot guys! I am bit worried here, since it happens totally randomly.
I am on Windows 7 64bit running ID CS5 with all patches.

Alright, I checked the seperations, all text appears to be on the K channel, nowhere else.
However, the text appears to get anti aliased with the upper method (subpixel AA) only on layers that contain NO transparency. I checked that with the Flattener Preview and only on pages without transparency I see a difference.
So what should I do now? Does it affect my printing results? Or should I change the flattener settings? (I would rather not touch that)
Thanks a lot so far! Happy to hear more.

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Varying black intensity in PDF/InDesign preview - any ideas if harmful?

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