I came in in April 07 and got a bonus. Got the first part in August after got to my unit and they processed the paperwork. I am now on the wieght control program, and even worse have a broken leg. I made excellent progress and was over by one percent prior to breaking my leg after last tape. I believe I was flagged, will this affect my future bonus payments, like the one that is due in April 08?

No, flagging actions fo not effect installment payments of enlistment bonuses.