I had that problem too with Tomcat 5.5.7, Axis 1.2 and jUDDI 0.9rc3,
but I've solved it.
I think that the solution is getting the right JDBC for MySQL.
Try this:
http://dev.mysql.com/get/Downloads/Connector-J/mysql-connector-java-3.0.16-ga.tar.gz/from/pick
because I had that problem with the last connectorJ recommended (3.1).
You have to put the .jar in your classpath and into the
<TOMCAT_HOME>/common/lib dir.
Here is my server.xml file and my juddi.properties file. I don't
remember very well what I've modified to make all work, but I think
that looking at differences between these files and yours you could
find the way to make it works.
Sorry if I can't be more precise, but I made it in a hurry due to the
hard work I had to do for my thesis.
I hope these infos can be useful.
Here are the files:
---- server.xml ---- (inside <TOMCAT_HOME>/conf)
(put this Context element inside the Host element "appBase=webapps
name=localhost")
       <Context
                path="/juddi" docBase="juddi" debug="5"
                reloadable="true" crossContext="true">
          <Resource
                name="jdbc/juddiDB" type="javax.sql.DataSource"
                password="juddi"
                driverClassName="com.mysql.jdbc.Driver" maxIdle="2"
                maxWait="5000" username="juddi"
                url="jdbc:mysql://localhost:3306/juddi?autoReconnect=true"
                maxActive="4"/>
        </Context>

---- juddi.properties ---- (inside <TOMCAT_HOME>/webapps/juddi/WEB-INF)
juddi.operatorName = jUDDI.org
juddi.maxNameLength=255
juddi.maxNameElementsAllowed=5
juddi.maxBusinessEntitiesPerUser=25
juddi.maxBusinessServicesPerBusiness=20
juddi.maxBindingTemplatesPerService=10
juddi.maxTModelsPerUser=100
juddi.maxRowsLimit=10
juddi.auth = org.apache.juddi.auth.DefaultAuthenticator
juddi.dataStore = org.apache.juddi.datastore.jdbc.JDBCDataStore
juddi.uuidgen = org.apache.juddi.uuidgen.DefaultUUIDGen
#juddi.monitor = org.apache.juddi.monitor.jdbc.JDBCMonitor
juddi.cryptor = org.apache.juddi.cryptor.DefaultCryptor
juddi.validator=org.apache.juddi.validator.DefaultValidator
juddi.dataSource=java:comp/env/jdbc/juddi
# jUDDI-managed ConnectionPool properties (Optional)
#juddi.useConnectionPool=false
#juddi.jdbcDriver=com.mysql.jdbc.Driver
#juddi.jdbcURL=jdbc:mysql://localhost/juddi
#juddi.jdbcUser=juddi
#juddi.jdbcPassword=juddi
#juddi.jdbcMaxActive=10
#juddi.jdbcMaxIdle=10
juddi.proxy.adminURL = http://localhost:8080/juddi/admin
juddi.proxy.inquiryURL = http://localhost:8080/juddi/inquiry
juddi.proxy.publishURL = http://localhost:8080/juddi/publish
juddi.proxy.transportClass = org.apache.juddi.proxy.AxisTransport
juddi.proxy.securityProvider = com.sun.net.ssl.internal.ssl.Provider
juddi.proxy.protocolHandler = com.sun.net.ssl.internal.www.protocol
juddi.httpProxySet = true
juddi.httpProxyHost = proxy.viens.net
juddi.httpProxyPort = 8000
juddi.httpProxyUserName = sviens
juddi.httpProxyPassword = password

I deleted the comment line to make this loooong message a bit shorter.

Cheers,

Francesco

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