I recently quit my job as a manager of a restaurant. I gave my two weeks notice and worked out the notice to the final day. When talking to a member of the upper management on my last day, they reminded me that I would be losing out on my fourth quarter bonus from 2006. This is due to the bonus policy stating that the employee(me), must be working for the company at the time that the checks are issued. I personally know of other managers who left the company and still received their bonus checks when they were in the same situation I am in now. Can a company choose to follow the policy on one employee, but then payout the bonus to another person in the same situation??

That depends on (a) the reason(s) they use to determine who does and does not receive it and (b) the terms of the bonus agreement.

I talked to the person in our home office who actually deals with the bonuses, and she told me that they had given out bonuses to people who "left on good terms". The terms of the bonus program are that the employee "must" be an active employee at the time that the checks are issued.

Unless you have a valid and supportable reason to believe that you did not get the bonus while others did BECAUSE OF your race, religion, or other protected characteristic, I'm afraid you're probably out of luck. The fact that they made exceptions for others does not obligate them to do so for you.