Are the instances sharing a registry or do they both have their own?
You can configure the data source for juddi by editing jbossesb.sar/juddi-ds.xml so that the two environments don't use the same registry database.
Yeah, I came to that conclusion too, after a couple of days of searching. I wish I asked the boards earlier. ;-) I'm having other database problems now though so I can't definitively say if this was the problem.