Here is a work around as long as you don't use the reader in an online class. This opens another Acrobat Reader window outside of IE 8 but it works everytime. It seems this is tied to Acrobat 9.x only. Acrobat 8 does not have the issue.
This way would be good if you had tried that. Of course, it may be the problem of your PDF files, maybe the links are crashed. If you view PDF files on the Interent with adobe reader, you may not open the link because it is disable for unknown reanson. I have come across that situations.