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The notice was most likely generated before the check cleared your bank, most likely few days before. Does the notice offer any explanation about the changes made to your return? There's a discrepancy between what you paid and what IRS claims you owe.
If your check cleared the bank and it is for more than IRS claims you owe, than you will be all right. It can take couple or three weeks before the payment is posted to your account after it cleared your bank. It is not unusual if you mailed a check to IRS.
The best time to contact IRS is before 9am other than Monday or Tuesday. An average waiting time is about 30 - 45 minutes, depending on day and time.
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