There have recently been many reports of the Java navigation pane in SA Publisher reports not loading when the version of Java on a machine is upgraded to version 7 update 25. SA Publisher was updated in System Architect 184.108.40.206, which was just released, to account for the changes introduced in this version of Java. If you have seen this problem, you can update System Architect to allow the navigation pane in newly created reports to work. Existing reports can be fixed by renaming the following files in the report's folder and replacing them with the files of the same name from the ...\System Architect Suite\SA Publisher\Common folder in the 220.127.116.11 install:
Incidentally, 18.104.22.168 also fixes a similar problem with the page generated by the SA Compare tool.