Keep settings is on by default when upgrading, like I stated before I usually deselect this option and load a config and packages after upgrade.
Because you did not deselect it is what I think is causing your problem
If you revert to 4.1.0 and keep the setting I believe you issue will still exist and you will need to do a setup from scratch anyway. I would do a complete fresh install of 4.2.0 or move to a Beta or Snapshot (Beta 4.2.1 release 3 has been pretty stable for me so far and I am moving onto snapshots as it has not been updated for a couple of days, meaning that there are no obvious issues that needed to be addressed. That being said I am sure a snapshot will come out for the weekend)