How to establish Benefit-Deductions with non-calendar plan years and changing pay periods.

I have a plan year for a Benefit\Deduction code that is not a calendar year. I have run it for one year that had 26 pay periods in it and it calculated ok. When I run it for the next year that has 27 pay periods it calculates a different amount. How do I fix this?

The reason this happens is because of the way that HR is designed to calculate a premiums. It takes the monthly amount x 12 and then divides by the number of pay periods for the year in accounting (Maintain>Payroll>Processing Groups>Pay Schedule).
 
If you change the number of pay periods, then you change the underlying formula.  Over the course of a year it should even out.
 
If you wish to adjust the calculation back to the way it was,  there are three options
1-    Navigate to Maintain>Payroll>Processing Groups>Pay Schedule and remove the extra processing group at the end of the year. This will return the number of pay periods back to the way they should be. At the end of the year, you can process the extra payroll as a supplemental.
2-    Manual Adjustments. You can change the figures payroll by payroll in Review\Modify calculated payroll or you can do an adjustment in Setup/Adjust employee balances along with a JV in accounting.
3-    Contract with your business partner or Abila Client Services to have a custom script written to handle your specific scenario.