Bonus Payroll Run using pay type set to calculate supplemental tax rate

 We have a Sick Leave Bonus run that the pay type is setup to calculate taxes using supplemental tax rate. Federal Taxes on everyone in this run has a Federal Tax amount of -1.00. We are using Vertex 2.9.6. What could be my problem, what am I missing. Payroll ID is setup with date range of from 12/27/2010 to 12/27/2010 with check date of 12/27/2010. Time card are dated 12/27/2010. We do not have the pay period setup in Master Pay Cycle. But on the Payroll ID the Period No. is set to a 3. We are bi-weekly and have ran the last check for 2010.

Any suggestion would be greatly appreciated.