There is a MAJOR bug in JavaRa - it erroneously trashes the JavaScript keys in the Windows Registry.
Fix/Workaround: If you have already downloaded JavaRa, unzip the contents and manually edit the file JavaRa.def. In the current download this file is dated 02-May-2011.
You must remove the following lines: 348 through 353, BEFORE running JavaRa
The lines to be removed contain the following:
HKEY_CLASSES_ROOT|JavaScript
HKEY_CLASSES_ROOT|JavaScript Author
HKEY_CLASSES_ROOT|JavaScript1