I have been running the same instance of BIRT Report Designer (Juno Release 2 - Build id: 20130225-0426). Last week I began having a problem running (viewing) reports as PDF or running with BIRT Viewer and then printing as PDF.
The report starts, displays the Parameter Dialog and then launches a white window with a small black square in the top left corner.
What does your report consist of? Are you using the internal browser? If so, you might try switching to use an external browser. To do this, go to Window -> Preferences -> Report Design -> Preview and check the use external browsers checkbox.