Professional GPS devices can be calibrated by allowing the entire GPS/GLONASS constellation contact the GPS device... this means having the GPS device active until all the individual GPS/GLONASS satellites have made contact with it. However, the GPS module found in mobile phones may or may not be at the same level as professional-grade GPS devices.
On the other hand, Windows Phones (when enabled in the locations settings) can store the location of the device regularly or just before the phone shuts down (in conjunction with the Find My Phone feature). This means that if the phone has made several "logs" at a certain location, the phone may easily recognize that location the next time a location-requiring service is launched in the phone - this, in some vague effect, may be considered as "calibration".
As for the inaccuracy, GPS and GLONASS devices need to establish un-interfered contact with the constellation of satellites. This means that the less obstructions there are in between your device and outer space, the more reliable the initial reading would be.
Are you launching your navigation apps from inside a building, a house, in a heavily tinted car, or where there are several high-rise structures?