A similar problem has been happening in Oregon with April 15th extension payments not showing up on clients accounts when the final tax return is filed:
"Thank you for sharing this recent practitioner experience. I checked with Megan Denison, Administrator for Personal Tax and Compliance Division, about this example. I learned that this experience can happen when payments and notices cross in the mail, or if payments take a little longer to post to an account. This is not uncommon, and it was explained that the best solution is to check the Revenue Online (ROL) account if a person receives a letter, to see if the issue is cleared up. "
-Marjorie Taylor, Legislative Director
Oregon Department of Revenue