The long running query logic in DQPCore uses millisecs when comparing to the query threshhold which is in seconds. It should both be in seconds.

// check if only need long running queries.
long elapsedTime = System.currentTimeMillis() - req.getStartTime();
if (longRunningQueryThreshold == -1 || elapsedTime > longRunningQueryThreshold) {
results.add(req);
}