Do you have a copy of the log JavaRa produces? That would assist in narrowing down the list of possible causes.
Have you contacted Bullhorn’s customer support to see if there are any current issues that could be affecting your service? JavaRa doesn’t really do anything beyond remove a pre-defined list of files/registry entries, so I suspect the issue lies in an incompatibility between the application you’re using and changes made in the latest version of the JRE.
As JavaRa does its thing almost exclusively in the registry; I system restore is very effective at reversing the changes it makes.