ManipUni said:
Lauch Microsoft Spy++ and use the "Find Window" tool. Drop it over the window and discover who is putting transparent windows in the middle of the screen.
I don't have Spy++ but I did find Winspector Spy: http://www.windows-spy.com/

It turns out that it's coming from Foobar2000, possibly foo_title.  I just shut down Foobar2000, and the symptoms have disappeared.  I removed dotnet_title.dll from my components folder, and it no longer appears when I run Foobar2000.