PDF looks different on iOS

My PDF form looks and acts differently on my iPad vs. my computer both using reader.
Has anyone else had issues? Or know of a solution?

Alec,
Thank you for the response.
No the blue and red boxes aren't the issue. Some of the issues include:
The dropdown box doesn't change other fields like it does on the desktop version.
The radio buttons at the bottom have changed possition.
Some text that is displayed on the desktop version isn't showing in iOS.
Do you see the same problems when you open the document in iOS vs. desktop?

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PDFs look different in Adobe reader and Acrobat professional compared to the built in PDF viewer on windows 8

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I am experiencing a very frustrating problem and I can't find a solution to it.
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If you like click on my blue name and email me the files.
To attach screenshots here you need to park the images on another site like:
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http://flickr.com/
http://picasa.google.com/features.html#utmmedium=embed&utmsource=pwalogin
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PDF looks different on iOS

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