Elevation gain is exactly what it sounds like. It is the amount of positive elevation change you made during the activity. i.e., if you run up 50', down 12', and up 12', your elevation gain would be 50' + 12' = 62'. If the device that you are using has a barometric altimeter, then chances are good that the elevation data for two activities on the same course with different weather (air pressure actually, but that is affected by temperature and humidity) will produce different results. This is just a result of the technique used for measuring elevation.
There is also the possibility that, if using a device with a barometric altimeter, that the elevation detection is incorrect because of a failed sensor.
On the activity details page, near the bottom-left corner of the page, is an option to enable elevation corrections. If you enable elevation correction on two similar activities, they should both report similar results (but not necessarily exactly the same).
