JE 3.2.65 contains an important bug fix having to do with Two Phase Commit processing, as reported in this OTN Forum posting. Specifically, if a transaction is prepared, but not committed, it is possible over the course of multiple recovery invocations (re-opening the JE environment) to have the transaction disappear (thereby preventing it from ever being committed). If you're using distributed Two Phase Commit transactions, you'll want to pick up this release when it's available.