When using named instances you will need to specify the URL slightly differently in the connection properties.
First off, try:
<url>jdbc:jtds:<server_type>://<server>[:<port>][/<database>];instance=<instance_name></url>
This is specified at the JTDS FAQ
If this doesn't work, try dropping the instance name, and changing the port to the port used by the named instance:
<url>jdbc:jtds:<server_type>://<server>[:<instance_port>][/<database>]</url>
Note. This port is different to the normal SQL Server port as each instance listens on a different port.
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