The cal files are not applied to the measured impulse response, only to the frequency response plots derived from it (and phase plots in V5). There are a couple of reasons for this, one being that if you get cal data for a mic (or soundcard) after having made measurements you can go back and apply the new cal data to those old measurements. Another issue is that to properly apply the cal data to the impulse response you really need phase as well as gain data in the cal which is less often available, although it is possible to make the assumption the cal response is minimum phase and generate phase info from the frequency response. A further issue is that attempting to calibrate out the LF rolloff which is inherent in most devices and measurement chains can lead to boosting LF noise in the impulse response.