We've recently upgraded to 4.6 after being on 4.1 for quite awhile. Problem is we can't progress workflows and the trigger manager doesn't work it is under construction and enabling it doesn't have any effect. The root user is also under construction.
Has anyone come across this before?
The trigger manager and root user are always in an under construction status. Can you provide some further information on what you mean by "can't progress workflows" and "trigger manager doesn't work"? Also, I would strongly suggest upgrading to 4.18 since 4.6 is now outdated.
The "Trigger Manager" asset is set to "Disabled" at the start of an upgrade using the automatic upgrade scripts and reenabled at the end - if it stayed disabled that suggests to me something went wrong during the upgrade, aborting the upgrade part way through and probably leaving a few things in inconsistent states.
If you've got any logs captured during the upgrade you should review them, otherwise you may be stuck with comparing the current instance against a restored backup of the old one.