Help my brother figure his pay statement...

My brother was recently required to give up a company provided vehicle and use his own to deliver small packages for a regional courier service he's worked for for many years.

He is getting a mileage reimbursement but that is being deducted from his other deductibles (FICA State + Fed etc.).

This I assume is going to leave him with a BIG tax bill at the end of the year.

Is this legal? Our bookkeeper and her friends have never heard of the reimbursement not being separate from the deductions.

Is this legal?

Who should we contact first? An accountant or lawyer in labor law? Our State AG's office referred us to the IRS but wasn't sure if that's where the answer would be found.