Hi Josh,
I just want to describe what I understand the issue to be please let me know if this is incorrect. You have a Swept Sine Express VI, and have configured it with two different Maximum sampling rates. You are changing the sampling rate under the advanced tab, and setting a different sample rate. You also change the Start and Stop Frequencies under the Sweep tab as you described.
When you make all these changes you see different frequency response from your circuit. I assume that you are expecting the same Bode plot, but can you give me a bit more info about what is going wrong with the measurement. Screen shots of the difference in the plots could help us identify what is causing your difficulty. I agree if your sweep value is constant then you should not be seeing a big change in the bode plot, but i would need more information to see what is wrong.
I have not tried to do a two channel response measurement, and i don't think it can be done with an express VI, but I am pretty certain we can find a way to do this with the Sound and Vibration Toolkit API.
If you are not using the Express VI at all please post a screenshot of how you have setup this code, or let me know what example program you started from and I am sure we can find a resolution to the bode plot behavior you are seeing.
Have a great day,
Michael D