@viveksingh Generally this is going to be something related to the service account and/or a service running the job versus a logged on user, that is where I would focus my search for the culprit, but you will likely need to engage the DBAs for the DB as well to help you try to sort things out, as they are going to be the experts on any settings in the DB side that may be in play related to things being run from a service call versus a logged on user request. Not sure what type of connection you are using, but if you can turn on logging for the connector, that should likely provide some additional information regarding things too. Sorry I do not have anything better, but these are generally environmental issues, not really anything wrong with the product on our side.
One other thing you can do is compare a script log from logged on user run to the service/QMC run and that should show you exactly where things are taking longer by checking the timestamp deltas for each portion of the reload, I would suspect if I am correct, only the calls to the DB are going to show a slower run-time etc.
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