Links inside PDF open with Reader app, but not IE plugin. Why? Help!

I am including some PDFs on a dvd. I link to them from a webpage also on the dvd. Some of these pdfs have links to other pdfs on the disc. While testing, one machine opens the main pdfs in the Adobe Reader application and their links work fine. On another, the main pdfs open with the Reader plugin for IE and none of their links work. What would be causing this?

I'm still testing, but I'll try and create some sample pdfs. I'm not sure how the ones I'm having difficulty with were created. I suspect Word and then converted using Distiller, but not sure. Thanks for your offer.
So far I've tested a number of machines with inconsistent results. Works on an XP machine running IE7 and Reader 8. Doesn't work on an XP machine running IE8 and Reader 9.4. Works on a Windows 7 machine running IE8 and Reader 9.4. This is getting confusing.

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