The Calibrate_DSA() function uses an onboard voltage reference to calibrate the analog input circuity of the DSA device. If the calibration of your board appears to worsen after a call to this function, it may indicate that your onboard, internal voltage reference is off.
Try doing an external calibration with a high-precision voltage source connected to channel 0 of your 4451. This is a way you can calibrate the onboard voltage reference, which will allow you to do internal, self-calibrations in the future.