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After modifying derby source to divulge the source of the null I have found that a LOB field (in this case 'data') is being set to object 'null'. Here is a snippet:
Element 1: begin parameter #1: null :end parameter ....
update lob set data=? ....
at org.apache.derby.impl.jdbc.EmbedPreparedStatement.executeBatchElement(Unknown Source)
Prior to 4.2.1.Final this was an empty byte[0], which is what I am actually setting in code. Somewhere along the line the empty byte array is now being set as null.