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The only thing I can think of that is changed to the system when a capture is running is that the interface(s) on which you capture are put in "promiscuous mode". You could check if this is what is changing the app behavior by disabling "promiscuous mode" in the capture options and then start another capture.
If the response time is still 30-40 seconds in this test, it would be interesting to see the difference in the capture files.