After reading your post again, I'm still a little confused. I'm going to state what I think is going on, and maybe that will clear things up.
I've seen weird things like this before when I've left MAX running on the PC, and then turned off my PXI/SCXI chassis and changed hardware.
When MAX first starts, it sets all the gains/filters that you have set for any cards. If the chassis is turned off and back on, and MAX hasn't been restarted (or a property of that card hasn't been changed), it will assume that all the settings are the same, even though the default state of the card may be different (like a gain setting).
This may explain why you are seeing what you are seeing.
I usually use MAX only to determine that my card is working. If you are using
LabVIEW (or some other programming language), I make it a practice to set the gain and filter settings when I'm setting up the acquisition. That way, I can be assured that NI-DAQ will reset the boards to the proper settings, no matter their default or current state.
I would bet that if you practice this in your code, you will not have these problems you are seeing in MAX.
Also, make it a habit to exit MAX whenever you are changing hardware.
Mark