That's because Moonlight hasn't reached full Silverlight 2.0 compatibility. The Moonlight team has said that they're trying to release updates for the beta on a weekly basis, but it's been a bit longer since they released Moonlight 2.0 Preview 4 (which is really Moonlight 1.9.3).
Sadly, there's no real guarantee that the Photosynth viewer will work in Moonlight 2.0 until it gets out of beta status (currently scheduled for September). (see http://www.mono-project.com/MoonlightRoadmap )
You can keep up to date with their progress on Silverlight 2 compatibility at:
Hope to see you up and running soon!