Given that a competent DAC (and they nearly all are) already manages - without PC side upsampling - flat frequency response, and inaudible noise and distortion, then we can conclude one of the following is at play.Thus far the upsampled audio changes ranges from subtle to none.
1 - You've managed to find one of the very few incompetent DACs that is creating massive (and hence audible) distortion.
2 - The filters you are applying are creating audible distortion.
3 - You are listening to the effects of your brain, and not of the signal (perceptive bias)