It sounds like you have all the code updated, but the Data has not been migrated. When you go to the ZMI, does it tell you that your Plone site is out of date and needs to be migrated? Try to run the migration.
I'm guessing the migration will likely fail, if you are trying to go straight from Plone 3 to Plone 5. See https://docs.plone.org/manage/upgrading/intro.html#no-large-leaps, and check out the rest of the upgrade guide there in the docs for more tips.