The Summit Group has run into an issue where the Negative Deduction in Microsoft Dynamics GP 10 and GP 2010 is Not Calculating on Checks After 3/25/2011 Service Pack Applied.
They have a recommended workaround.
Negative Deduction in Microsoft Dynamics GP 10 and GP 2010 Not Calculating on Checks After 3/25/2011 Service Pack Applied » Summit Group Software Blog
Microsoft & the GP EcosystemPayables & ReceivablesPayroll & HRGP 2010GP 10
Archived post from 2011. Dynamics GP and the links it points to have changed since; check current documentation before relying on version-specific steps.