Acrobat Pro breaks MS work links to company file system.

Hello Folks
I am putting together a large PDF technical manual from many individual MS word 2010 documents.
These MS word documents have many links to various places on the internet, company intranet website as well as to the company file system. When I build the initial PDF from all these word documents all the links work just fine. Its only when I upload this PDF to the company website AND the PDF is opened within the browser (IE) do any of the links pointing to files or folder on the company file system break giving me 404 page not found errors.
Now if I refrain from using Acrobat and just save as PDF within MS word and then manually combine the files into the final document these links work just fine after this document is uploaded to the company’s internal website.
If I hover my mouse over these troublesome links I see file:// (path to link) when I save as PDF in word. When I build using acrobat I see nothing when I hover over the links but the link still works until it gets uploaded to the company internal website and the file is viewed within the browser.
Because this manual needs to be viewed by many employees and the default setting in adobe is to open within browser I really need this document to work properly when viewed in the web browser. Using save as PDF in word, then combining 300 + files is going to be tedious if one of you fine people cant point me in a better direction.
Anybody ever encountered anything like this??
Thanks for any help you can provide.
Chris

Another Update:
The problem already exists in Visio 2002: in fullscreenmode the links are already working incorrecty that is to say non-link-areas of the page are clickable.
I paste a simple dynamic connector on a sheet and make it a link. In fullscreenmode areas around the connector work as clickable links, too, the same for the PDF. So it seems to be a Visio problem only with the Shape "dynamic connector".
Any ideas possibly?

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