The .wxs, .wxi, and .wxl extensions were probably already mapped. I only mentioned that because I couldn't remember whether I had added that mapping myself or whether it was already in there.
Turning off the auto validation did not correct the problem, but I just now noticed the following error message:
Error processing DTD '
http://schemas.microsoft.com/wix/2006/wi' for file 'b:\Projects\WiX Source\src\ext\UIExtension\wixlib\FatalError.wxs'. Socket timed out.
If you want to work off-line, use the URL Mappings dialog ("Tools","Options","URL Mappings...") to map a URL to a local path containing the files.
I don't fully understand the message, or how to rectify it. Is there something else I can disable to prevent this processing. If all else fails, I suppose I could remap the file extensions to plain text, but then I lose the syntax coloring.