They are checking that there is no discrepancy between what your seeing on your altimeter and what they are seeing from your altitude encoder. As I said before, if there is an issue with your static system this will affect both (quite possibly by the same value).
Talking about the static system when the topic is about instrument calibration is a bit of a thread drift and I apologise for that.
Last edited by Check_Thrust; 9th Jan 2015 at 22:36.
Reason: Typo