The elevation change definitely plays a role, but it isn't going to be night and day. I've opened some of our cans (packaged at 9300 ft) at sea level and the carbonation is only a little low. Theoretically, that should be a difference of about 0.3 vol.
How big a micro are they? If they're filling by hand (on a Cask system, most likely) they may not be getting uniform fills. You really have to baby-sit the manual fillers. If you can, check a full can by weight. It should be 374 g. Anything under about 360 g and you're going to see a noticeable change in carb levels, IME.