Can you share more of your log, certainly this seems to be an issue, but normally the data move happens in parallel with separate connections so it doesn't get this issue.
Can you share with more of your log file, so we can diagnose this some more?
I did a small test mysql migration with several large test tables on 4.0.2 with no issue.
Please provide: Your log, Versions of: mysql driver, mysql database, SQLDeveloper.
Note SQLDeveloper migration repository requires 11g (can be 11g XE).
If the issue is database dependent - a create script for test database would be ideal.
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