A question on AEM SQL 2 Query Limit settings

Hello folks,
We have an AEM Scheduler which executes some query and get the results. Usually we check the query which it going to form in real time and execute in queryPerfomance tool to understand which index it picks and if need be we reindex the custom properties. Basically we fine tune it before considering to execute from the Schedulers/Servlet/WFs.

Offlate we observed a strange behviour where the query which executes from code takes almost 500s whereas the same exact query if we run in the queryPerformance tool it is just 2 ms, in the same instance and at the same time. 

Anyone know do we have different settings for the one which runs from the bundle/code and one which runs through queryPermance tool? 

<your-domain>/libs/granite/operations/content/diagnosistools/queryPerformance.html

Thanks,
Mrudul

@7650794