At the moment, because the design of the mail file has not been upgraded to 9.0.x, our test users are able to open their mail using the icon on the workspace, not the iNotes link.  In initial testing it was determined that although this is not as intended, this is how it work, but once we upgraded a test mail file to 9.0.x this method failed and we had to use iNotes.

Not sure how they were able to open the 9.5.3 mailfile.  We never allowed opening any version of the mailfile in Notes Browser Plug-in.  The method of checking is that if it's what's specified in the location document, then we won't allow.  So did the users get around by changing the location document to point to some other?  Also the 9.0.1 design of the mail template has a checkbox on the 1st tab of the infobox.  But in reality, mail access is disabled in NBP to your own mailfile.  When user double-clicks on the workspace icon, we build a iNotes URL and then fire that off in the browser.  

 So within the corporate network, a user has no issue opening their mail or any other database. I am assuming this is an iNotes URL.  You should check the URL being used at this point.   However, if outside of the network, mail doesn't work yet other databases can be opened.  The servers are Win2008 and port 80 has been opened on the servers.  When trying to open mail from outside the WAN, the error displayed on the browser is "this page cannot be displayed" and says to make sure the web address is correct, which it is.  This would be the same web address that other databases are being opened from.  Is there something that needs to be opened on the server firewall or the corporate firewall? Can you check the URL at this point and see if ti's the same URL that worked when in office?  If this is the case, then the Notes Browser Plug-in is working correctly, but something in your network setup that's not allowing the browser to get to the url.