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Yeah, speed is the only thing I can think of. You aren't doing any threading or anything like that, are you? Because it could be something like race conditions if you are. Where is the ArrayIndexOutOfBounds being thrown from? I suggest you do try/catch around all errors, and write them to disk so you can check them out later.

Also, avoid testing against Raiko (mini) if you can because it saves data. Rather test against RaikoMicro, or do something about that data-saving, like modifying Raiko or deleting the files each time.