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I’m confused

Caching Question For DBAmp

I am working a project that requires numerous queries to be executed at Salesforce using DBAmp. The queries are timing out.
I am querying many different objects one after another. It seeme to be the case that when i run one alone in a new window, it runs for only 5 seconds. When i run another in the same window often times it will run so long that i give up any hope of it being successful.
The basic idea is running a select count(id) from each object. Some objects have a few million records, but getting counts should not take that long.
So could it be that the window is caching the queries and results and getting stuck when trying to execute the other queries?
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