Let's go over the steps on how you can properly record a payroll liability refund check.
First thing I'd suggest is to run the Payroll Liability Balances report.
How to enter a payroll liability refund check:
For other situations you might have with recording a payroll liability refund check, take some time to view this article: Record a payroll liability refund check. It shows the steps for when the taxing agency has withheld a portion of the refund for a different balance due, as well as an interest paid to you on the check.
If ever you need further assistance, let me know by posting it in the comments below. I'll be sure to get back to you.