In case you havent found a solution to this issue, here is how you edit the balances of any of your accounts. I was having the same problem as you and noticed that other people were as well.
This worked great for me as I was able to edit any account and bring everything back to $0.00 balances without deleting the business profile which I had already created!
1. Find out which accounts are still reporting an open balance (even though you have deleted any applicable invoices) - Reports > Balance Sheet... > View
2. If any of the items listed in this report are showing a balance, note their account number and go to View > Chart of Accounts..
3. Open the account you would like to clear or mofify the balance of and change the "opening balance field". If any of these accounts show this field as greyed out (not editable), in my case it was 'historical balances'... proceed to step 4!
4. Back up your current data - Accounts > Back up Data... > Backup to removable drive > Select some place ie: your desktop
5. Navigate to the 'Accounts' folder inside your backup folder (ie: c:\...\...\desktop\ExpressAccounts-Backup-2012-XX-XX\Accounts)
6. Select the account number of the desired account you with to edit and use a text editor such as Notepad++ or simply notepad to edit the account file
7. Notice the balance will be in a couple of locations within this file so make sure you edit both locations to whatever value you prefer (ie: "0") and save.
8. Restore your backup! - Accounts > Restore Data... > Restore from Backup > 'your backup directory here'
9. Run the report for your Balance Sheet again and behold your new (proper) balance!