I have this problem for standard users, that is, not Admin level. Admin level users have no problems.
If a web site opens up a pdf file with java, usually in a new window, and the file name is very long (I haven't figured out how long, but visually long) then the reader plug-in won't work and opens a blank page. If the file name is small then there is no problem, and reader opens the pdf without problem.
Interestingly, if I edit the document name (say for example the link has something on the end like "&Doc_Type=Statement" which is obviously not part of the document name but part of the SQL used to find the document by the web page) then reader will open the file no problem.
Again, this doesn't happen for Administrative level users.