Hello monicarojas,
I'm pretty sure that the gain is being applied when you use the input limits. It may be that you think the VI will return you the amplified value, which is not what the driver does. Instead, the driver will amplify, digitalize, and then the software will divide, -before giving you the measurement-, the digitalized value, so YOU WILL ALWAYS GET THE REAL VOLTAGE (NOT THE AMPLIFIED VALUE).
Example:
daqcard with gains: 0.5, 1, 2, 5, 10, 20, 50, 100
input limits = +/- 1 Volt
In this case, the driver will choose the maximum best gain to be applied, in this case, gain will be 10 (considering the input limits the user set to +/- 1, a bigger gain could potentially saturate the ADC's input, which is +/- 10)
if you input 0.33 volts to your board, it will be amplified x10 times, so the ADC will get 3.3 Volts at its input, will convert, and give back the digitalized value. Then, the driver, as it knows that the gain applied is 10, it will divide 3.3 before giving it to you, so your vi will return 0.33 Volts.
I hope this clarifies your question,
Regards,
Jorge M.