I have been working on a Silverlight app (using VS2008 and Blend June Preview), and I first noticed that, sometimes, when I ran my app I did not have the latest code, so I stopped, rebuilt, and restarted the app and it usually worked.
But this week, I have been blocked for an hour when my Debugger suddenly stopped working. I thought the changes I made introduced strange behaviors causing the ASP.NET Development Server to stop. Then, I realized that for some reasons my latest code was not cached anymore by IE!
So, if your Silverlight app does not appear with your latest changes, or if your Debugger suddenly stops working, clear the "Temporary Internet Files" in IE ("Tools\Delete Browsing History..." menu).
UPDATE
Since this also happens when I update the structure of my solution (moving project in sub-folders, etc.), I also need to check the Properties of my Web Application. The "Silverlight" CheckBox should be checked under Web / Debuggers.
Links:
Silverlight.net Forum - Debugger stopped working
Silverlight.net Forum - aspx file not displaying the last .xap build