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The case you describe is not familiar to me, but you may want to review this thread with a similar error:
java.sql.SQLRecoverableException Io exception Size Data Unit (SDU) mismatch
The comment there about a "recent JDBC driver upgrade to ojdbc6.jar" is interesting. I encountered a different error within the past couple weeks (can't recall exactly what), but noticed that the ojdbc6 jar files in 64-bit SQL Developer 3.2.09 and Instant Client's do not match. The SQL Developer jar is newer. Copying the one from the Instant Client (126.96.36.199) and replacing the SQL Developer version (supposedly 188.8.131.52 also) fixed whatever issue I faced. Comparing the manifest.mf files shows this:
This is just my best guess at this point.
ojdbc6.jar from SQLDeveloper 3.2.09.23 64-bit -> Repository-Id: JAVAVM_184.108.40.206.0_LINUX.X64_110829 ojdbc6.jar from Instant Client 220.127.116.11 64-bit -> Repository-Id: JAVAVM_18.104.22.168.0_LINUX_120621
Let us know if this helps,
SQL Developer Team