Why do my loops slow down after many iterations

My Vi seems to freeze up or slow down after several iterations of the loop. This is an Analog Input Capture VI.
Attachments:
Final_Main_VI_with_working_amp.vi ‏456 KB

First of all, thank you for your contribution. You are right to say that I have no need in changing the AI Config every time that the loop runs. But as this is supposed to be a soft-scope, I need to be able to update the parameters associated with AI Start while the loop is running (e.g. trigger level).
I have tried to move the AI Config subVI out of both loops but the error as a result is: "No transfer in progress for the specified source."
I also need a sampling rate of exactly 96kHz. I realize that the laptop clock cannot attain this value. Do you know how I could get exactly 96kHz.
Attachments:
Final_Main_VI_with_working_amp.vi ‏498 KB

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