I found another work around. From the system where I cannot see the decision
tables under the package, I can use the guvnor import/export tool to export the
repository and then re-import back into the same system and the decision table
appear. I'm guessing that the guvnor import tool is recreating the repository
from scratch and sees that the decision table belong to the package and
recreates this link.

The problem with this solution is that the app server were the guvnor tool is
deployed has to be running in order to use the guvnor import/export tool.  I'm
deploying guvnor war with my application ear and my application depends on the
rules existing. I'm looking to create a base line version of my decision tables
and to deploy this version with the application.

The way I went about doing this was to capture a backup of the repository stored in the
database using a database tool (meaning outside of guvnor) and then to restore
the database on other system without having to worry about the contents of the
JackRabbit repository folder on disk, except for the repository.xml and the
default workspace.xml file. 

It also seems like if the storing repository in a database that it is not enough
to just backup the database. You would also need to backup the JackRabbit
repository folder to go along with the database backup.

Any advice on how to do this would be greatly appreciated.

Thanks,
Guy