This has been a problem with my laptop when working with files on a network mapped drive for months. In my experience this isn't limited to vista, office sp2, or SEPM MR1 or MR2.
As with delifeath, if I disable auto-protect it usually goes away but not always. The problem seems to occur less frequently with SEPM MR4 MP1, but it's still there every now and then. I have tried to find the steps to trigger this problem but I haven't been able to as of yet.
Saving to our desktop and then uploading it to the server isn't really a satisfactory workaround. This can create problems if two users are making changes to the same document (stupid I know, but it happens).
Edit: Erik, can you provide any details about this microsoft security measure or are you talking about the Vista application control?