I'm not quite sure of the exact conditions under which clearBindings is called with a non-empty set of updatedBindings, but it appears to happen during the (very complicated) save sequence in WebDAVFS on OS X 10.3. The delete semantics in MySQL 4.1 are different from MySQL 4.0. This problem has mostly been solved with the addition of the MySQL41RDBMSAdapter, but it looks like additional delete statements were added to resolve bug #30442, and they weren't overridden in the 4.1 adapter.
Created attachment 13395 [details] Patch file for MySQL41RDBMSAdapter, MySQLRDBMSAdapter and StandardRDBMSAdapter
The easiest way to fix this problem is to copy the clearBindings method from MySQLRDBMSAdapter to MySQL41RDBMSAdapter, but the 4.1 adapter is already duplicating a lot of logic simply to replace the table name in the delete statements with aliases. The proposed patch is a refactor of StandardRDBMSAdapter and MySQLRDBMSAdapter that creates a callback method to create the standard delete statements. MySQL41RDBMSAdapter simply overrides this method to delete the alias rather than the table.
Patch applied to CVS HEAD.