Microsoft has received reports of compatibility issues with Nikon NEF files after installing version 1.0 of Nikon’s RAW codec posted in January 2007. Tagging the RAW files through Windows Vista or the Microsoft Photo Info tool after the codec is installed appears to cause these files to become unreadable
in other applications, such as Adobe Photoshop. We have confirmed that these files can still be opened with Nikon Capture. [via Microsoft's Photo Info FAQ]
Also, there are posts on this topic at the Microsoft Photography Blog.
Admittedly, I haven't done tons of reading up on this since, even though we have it, I won't be upgrading to Vista probably until we hit a period of time when our load is a bit lighter later this spring or early summer. But this looked like something of which people should be aware. And, it looks like I'm coming to this about a month late - the articles are all dated early February.