This is a known issue. The IRS is way behind in processing payments. 

Can we stop the efile of the payment to IRS and just send in a check?  Don't want to double dip into any account.

Call IRS e-file Payment Services 24/7 at 1-888-353-4537 to inquire about or cancel your payment, but please wait 7 to 10 days after your return was accepted before calling. Cancellationrequests must be received no later than 11:59 p.m. ET two business days prior to the scheduled payment date.

Can tax expert from TT answer this question? It is important to know what is happening