I've thought about that. I don't necessarily think he would blame me for it, but I might just be naive. At any rate, I do have several people who can back me up if that were to happen, including some of the company shareholders and my previous boss (who left when the current boss started consulting with this company several years ago).
This whole thing started when they were changing over all of the medical staff from independant contractors to employees, and they wanted to keep it all "cost-neutral" so I think THOSE employees were aware that this would be the process (instead of decreasing their regular hourly rate) and they were ok with it. However, this has continued to be my instructed procedure for doing everyone's payroll, which doesn't make sense to me for brand-new employees who were never contractors to begin with.
Most of the full-time employees don't even notice -- they have other legit benefit deductions every month so they're used to their "gross pay" being kind of... fuzzy. It's the part-timers who call me, wondering "I don't have any benefits or expenses, why doesn't my actual earnings match what is being reported as my gross pay?"
I don't discuss this with any of the employees. If people have questions, I refer them to my boss. I just have to deal with the vaguely "icky" feeling of doing something that I'm not entirely sure is ethical, month after month. I guess I just needed some idea of whether this was a big enough issue that I SHOULD be reporting it.