This has caused employees, in some cases, to inquire as to where their penny is :). How do organizations typically alleviate the difference in calculation issue? Any suggestions?
The typical approach is to have a single, sound method of payroll calculation.
And if for whatever reason there is a known systematic error in the computer programming that you won't or can't economically fix, then you acknowledge that state of affairs publicly to the employees, and either make a manual correction or apply a setting to the automatic calculation that results in an excess in favour of the employee.
I think a lot of bosses misunderstand that the issue is not always the quantum of error, but their fundamental attitude to the accuracy of the payroll.
We've almost all dealt with bosses, at some point in our lives, who thought they could renegotiate the payroll as they went along, who seemed think paying wages accurately and on time was not on their priority list, or who thought they did not need to employ a competent clerk to execute the payroll.
I suspect the fundamental problem here is that you're advertising a certain "salary" and then in fact calculating basic pay on an hourly basis. It might not be so much that the calculation is wrong, but that internal decimal amounts are insufficiently precise to express an exact yearly salary as an hourly amount. In that case, calculate your basic pay as a fixed salary amount instead, and only drop into hourly calculations if necessary to partially deduct or enhance the salary amount.
Above all, taking the issue seriously as a matter of principle when small errors do arise for the first time, will likely lead to much greater trust and forebearance if larger errors might arise.
It really isn't about the penny, but about whether you have the right attitude to a very important matter, in much the same way as the new employee waltzing out the door two minutes early isn't, if challenged, well-advised to justify himself to the boss by the small amount of time stolen, but to either ask permission for an allowance, or else sit back down for two minutes in a perfunctory way.