I think the reason for your problems are your wrong upgrade steps.
You missed to read this:
https://www.bestpractical.com/docs/rt/4.2/UPGRADING.mysql.html
You have to upgrade to 3.7.87, then run the queries from
upgrade-mysql-schema.pl, and then upgrade to 4.2.12.
Chris
Am 15.02.2016 um 18:08
I am trying to migrate an old RT 3.6.5 (installed by someone else) to
new FreeBSD server running RT 4.2.12 (freebsd package)
My problem is that after the update, the new root account lost its admin
privileges and I dont know how to restore them. I can still log with
this account, but it is not
