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What's it doing during these bad transactions? Is there a difference between what those are doing and what the fast ones are doing?
Off the top of my head with so little information, the only thing I can come up with is that a lock is being held which is delaying some of the transactions from completing until after the timeout hits.
ORA-01013 is the direct result of the timeout (your application server issues command.Cancel() after timeout is reached).
You have to raise timeout or make your transactions faster.