Just an update on this one I removed Enterprise Manager from the VBR server to clean things up. I then resinstalled it also creating a new SQL database. Now the Advanced Searching works fine and as expected. Not sure if there was something messed up during the upgrade/updates of the software but a clean install fixed it.
Just in case anyone else has this issue try this first. I know it is a pain as the database needs to populate again with backup jobs and restore points but this seems to be the best fix.