Resolution

Delete and re-add the pay code to allow the Base Pay box to uncheck and the recurring rate to calculate correctly.

Go to Employee Job/Salary (Payroll>Employee Maintenance>Employee Job/Salary).
Search for the Employee and Pay Code. Click Delete in the toolbar.
1. If in versions 2018.1 and higher, all instances of the pay code will need to be deleted.
Click Add. Define applicable fields. Click Accept.
1. The Add to Base checkbox will now show unchecked from Pay Master and the Recurring Pay will show as expected.

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