I would start with #2, the practice consultant. The employee is somewhat out of the loop. She asked for and received her bonus early. From her standpoint all was good. The payroll company did what they were told - pay the employee.
The question is what was the basis of the bonus and how did it become ingrained (i.e was a Christmas bonus made automatically into the pay structure without your knowledge). But you make mention of a monthly bonus - how is that determined and was this the monthly or the Christmas bonus. But you also state that you did not know about bonuses, I'm somewhat confused on this.
It appears you were inappropriately taken out of the loop. It appears to be through the practice consultant. On the surface there probably isn't any malfeasance. If the explanations of why you were not included are not clear enough from the the consultant, it might be worth having the accountant look for any other unexpected cash flows. (Then again, might be reasonable doing that anyway, just to make sure).
