Why the map is different when creating from logged file?

edit

Gmapping takes in a large number of scans, but ignores most of them in order to minimize computation time.

If you ran the bag file and ran gmapping, it is unlikely that you will get the exact same map because the scans that gmapping will process are likely to be different.

Another thing to consider. Does your bag file contain map messages? These wouldn't interfere with the gmapping algorithm, but the result on rviz would look strange because you're getting maps from two different sources.

If you recorded a bag without gmapping running, then played back the bag with gmapping running, you will probably get the same result each time you run gmapping because you are running it in a more controlled environment.