There have been lots of changes between versions from v4.1.1 to v6.0.1. If you upgrade directly you are bound to have some problems. A far better approach would be to upgrade to v5.1.2, then upgrade to v5.5, then upgrade to v5.6, then upgrade to v6.0.1. Various changes etc should be taken care of when the upgrade is performned.
If you are installing to a new machine, then first install v4.1.1 on that box and then restore from a backup and then do the various upgrades, one version at a time.
You would be wise to uninstall any add on contribs are these will most likely be incompatible with newer versions of e-smith/sme.