When 126.96.36.199 is first installed, it cleans up the database of the old wp_sessions that are no longer used in the new version. I suspect some users that had busy sites are experiencing a timeout while that cleanup happens because there is so many old session rows in the database. The next time you install it, it does not initiate the cleanup since it already happened and everything is fine.
You can manually cleanup the old wp sessions if you want:
The form data is stored in the database, so it should be there.
The error is concerning the visitor maps plugin, deactivate that one and update the other ones separately, then try updating it. Your server may not have enough free memory to update all at once since the GeoLiteCity.dat file is 30 Meg in size.