Just to be completely sure, how exactly have you done the upgrade?
The reason I'm asking is that when upgrading across multiple versions you actually need to run the site first after each upgrade because there is a script that is executed first time you run upgraded site and which actually updates database data. It seems to be that you haven't run the script and therefore some DB data is broken and this may be one of many issues you could encounter.
The way you should upgrade is this:
- 7 -> 8 + run site
- 8 -> 8.1 + run site
- 8.1 -> 8.2 + run site
- 8.2 -> 9.0 + run site
If you haven't gone this route, I'm afraid you will need to upgrade again from version 7 as there is no simple fix for this.