I wonder if it would shed any light on the issue if you separated the two? In other words, what would happen if you mocked up your MySQL connection and just generated "responses" for Lucene to index without having the database drivers even loaded?
Also, you could write the data from MySQL out to a flat file, say in some fixed format. If that worked, then index from the flat file instead of the database and see if the issue went away (I guess I'm thinking two separate programs here, up to you). At least that *might* give you a clue where the issue was. Note: I'm *not* suggesting that this is what you do in production, but since we're all stumped on what's going on, maybe this would help pinpoint where the problem is. Of course, in the unfortunate case that all the above worked, you're reduced to "something is wonky when the two try to play together", which isn't very helpful :(. But at least you'd be more confident that it wasn't something head-slapping obvious. FWIW Erick