That just puts an emphasis on what I said. If there are a lot of hidden things that can go wrong, then in any non-trivial application some of them do, and Java performance is on the average, horrible.

The bigger problem is that there's no reasonable way of figuring out what the problem might be.

And for the record, said code was a tight loop, created no objects, had the same kind of workload of a sort algorithm; The two nontrivial things about it was that it was accessing multiple simple vectors using the same index (non-idiomatic java), and that one of those vectors was a memory mapped buffer (non-idiomatic java, but essential because of the overuse of memory).