I had a similar problem in another context. There where two major changes from 
MySQL 4.0 to 4.1:

1. Authentication to the server has changed completly, so be sure to recompile 
all MySQL libs with support for 4.1.

2. Some SQL syntax has changed. Reconfigure JBoss to output all SQL statements 
it send to MySQL. Have a look at the CREATE TABLE statements and try them "by 
hand" directly inside MySQL. Fix those and then adjust JBoss db-scheme.

Good luck!

Alexander


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