Fixing hard System.exit call in DaxGenerator also added a defensive try,...

This pull request is a fix for a bug from SEQWARE-1451 and verified on the CentOS VM by the steps in https://wiki.oicr.on.ca/display/SEQWARE/2013/01/03/Jan+3%2C+2012%3A+Testing+SEQWARE-1451

I could not replicate the locking issue in the VM, but it is possible that the System.exit was causing JUnique to malfunction (or a cron issue) so let's see if this helps.