When you say that you have a desktop shortcut - do you mean that literally, that you created the shortcut from the original file location?
Or did you inadvertantly save the file to the desktop, as well as to a 'My docs' location?
It's been done many times before, and can be very irritating until you realise what's happening. I ask because you say "changes to the file via the desktop short cut never show up on the original file". Which leads me to think that the changes do show up on the desktop file - in other words you have two files.
Could that be a possibility?