That's OK. I have a Top Secret clearance ( or used to )
I don't think there's anything wrong with your website. My pdf links also behave the same way in Safari. However, in Firefox the pdf files appear as they should.
This is even with the PDF Browser plugin that's available so that PDF files can be viewed in browsers. So there's something that's changed recently that's preventing Safari from viewing PDF files.
Right now I don't have a solution. Well, there is a solution of sorts. That's using Google Docs Viewer to display the PDF document. This demo page has an example: Scrolling Text Box. It does not require a plugin.
You use URL forwarding with masking.
The pdfs do not display properly on my iPad.
They're scaled down and only page one of multipage files are visible and the pdfs cannot be saved.
When I use this is address :
the pdfs displays all pages correctly and they can be saved to iBook.
So why not use the domainname properly. But that may interfere with you other website :
You have to find a solution anyway, since MobileMe is closing down by the end of June.