How did you use Turbo Tax Self Employed to pay the last 2 quarters? Do you maybe mean QuickBooks Self Employed Version? Turbo Tax doesn't pay the estimates but can help you calculate the amount. Did you mail in the 1040ES estimate slips with a check?
And see this prior discussion about EIN vs SSN. It may help
https://ttlc.intuit.com/community/business-taxes/discussion/ein-vs-ssn/00/846902
