Nicole, we had several issues on the L4 upgrade to 6.0.1 including nDepth queries not working. Support Center and Development eventually fixed that.
The Reports issue is covered under case #708442, now closed, with the conclusion that it will take time to rebuild the headers before Reports can retrieve actual event data.
At the moment, the only report that returns any data is the Database Maintenance Report, but that seems to be talking about the 890GB AlertDB disk on the L4 Manager Appliance and not the 2.3TB AlertDB disk on the L4 Database Appliance. I just thought I would float the problem around the forum to see if anyone has had success with 6.0.1 Reports on a dedicated database/L4 appliance.