As noted earlier, a bug in JDK 1.6.0_04 and 1.6.0_05 breaks compilation in the Windows exe app. The bug has been reported to Sun, but they have thus far been unresponsive. As a workaround, the most recent Developer Release does not include the Windows exe app on the class path when compiling with one of the affected JDK versions. As a result, Windows exe users compiling JUnit tests will need to download junit.jar and place it on their class path. Hopefully this is a temporary workaround, and Sun will respond with a bug fix in a future JDK update.
UPDATE: Version 20080717 includes a full workaround; it is no longer necessary to manually reference junit.jar.