Well, the problem seems to be solved.
I tried a second download of the June Versio--this time from the site:
http://download.microsoft.com/download/4/D/5/4D55442C-D183-4F0F-9163-AD31A09BDFC1/Deep%20Zoom%20Composer.msi. I am not 100% sure that is where I downloaded from yesterday.
Anyway, I uninstalled the February 2009 version, which I had reinstalled since it worked for me, and then installed the June version from the above link.
So far, it is working correctly and creating the export to a Silverlight DeepZoom project.