Simple IRA Pretax contributions

One of our customers set up a simple ira for their employees. The calculations seem to be correct for all but one employee. After some head-scratching we figured out the company is set to match 100% up to 3%. All of their employees are set to contribute 3% except one who is contributing 5%. With the employee contributing 5% when calculating his payroll it looks like it is figuring 3% as pretax and the other 2% after tax.

Is this normal? I thought the whole amount up to the max was pretax.