The "durationMillis" in a slow query log looks at CurOp::elapsedTimeTotal, which doesn't factor in pauses. The latencies reported in the opLatencies serverStatusSection derives from elapsedTimeExcludingPauses. These two should be consistent.

Separately, I think it could be beneficial to remove the concept of "pausing" from the CurOp timer and fold it into the queues logic as suggested in SERVER-131015.