I had the same problem. I fixed it by Choosing Chart of Accounts, Edit Account, for the account I wanted to use that wasn't in the drop down list. Once in Edit Account, there should be two tabs at the top, one for General and one for Bank feeds. Choose, Bank Feeds and then choose the Deactivate box. Now, go back to upload the manual QBO file or connect for the direct feed and you should see now the account you were looking for previously but wasn't there. Try this first before all the other suggestions.
