I'm still new to ISPconfig, and I had the same problem when I moved sites from a reseller to (in my case) the Admin.
I moved things around so much that it must have fu**ed things up in the DB.
When I tried removing an empty reseler, ISPconfig told me thet I could not remove it as the reseller still had clients in it..
Clicking on the resellers name it showed empty for clients and sites.. The Recycle Bin was also empty.
When I loged in on the system as the reseller, it did also show no clients and/or domains! (Recycle Bin was also empty)
There was no way for me to delete the 'empty' reseller.. I ended up deleting all the domains (only 3), and emptying the Recycle Bin.
After this I could delete the reseller.