I can confirm the same problem with the jms tables. I missed out where they were generated from, but they are the ones causing the problem. When you drop those tables, at least the seam generate-entities will succesfully finish.
mysql> select table_name, table_schema from information_schema.tables where table_schema='foo';
+-------------------+--------------+
| table_name | table_schema |
+-------------------+--------------+
| HILOSEQUENCES | foo |
| JMS_ROLES | foo |
| JMS_SUBSCRIPTIONS | foo |
| JMS_TRANSACTIONS | foo |
| JMS_USERS | foo |
| TIMERS | foo |
| jms_messages | foo |
| user | foo |
+-------------------+--------------+
8 rows in set (0.01 sec)