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After discussing this some more with Tom (from JBossTM), I think the first question we need to answer here is how we view timeouts. Are they (1) error conditions? Or are they akin to rollbacks?
That will answer the "what we want to do" when we recognize that a timeout happened.
Personally I don't necessarily like throwing an exception here. First, we are really best guessing that the afterCompletion callback is due to a timeout; second, imho, we are performing functionality that JTA should be doing. However, I think it is essential that the user get some form of notification that the transaction timed out, and atm that is simply not guarenteed by the JTA spec, not its impls.