Problems opening PDF files after upgrading file server to 2012 R2

Hi,
At the weekend we upgraded our main file server from Windows 2003 to 2012 R2.
Since the upgrade, users (including myself) can only open one PDF document at a time from the file server. If I double click a PDF file, it opens like normal, however If I double click another PDF file, the acrobat reader flashes (in task manager I can see another instance AcroRd32.exe starts and then exits) but the second document doesn't open.
If I close the first document down, and then try and open the second one, then it opens with no problems.
This only affected opening files on the new file server, opening multiple files on a local drive is fine.
If I disable 'enable protected mode at startup' then I can open up multiple documents from the file server. I'd prefer not to have to do this.
The users are using Acrobat Reader 11.0.10 on both Windows 7 64bit and Windows 2008 R2 Remote Desktop.
Does anyone have any ideas what may be causing this? And does anyone have a workaround other than disabling protected mode?
Thanks
Joe

An update...
The new fileserver has a different name than the old server. We have a CNAME alias pointing the old name to the new name.
I only get the problem when accessing the PDF documents with the old name, when accessing via the new name, everything works as expected.
However there are lots of shortcuts and other other links to the old name, so finding a workaround would still be good.
Cheers
Joe

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