One department is allowed to take excessive vacation. How do we handle inequalities?

We are a small, 12 person start-up that is developing a breast cancer detection device. This device relies on a robotic mechanism and software. Of the 12 employees, 6 are software engineers. In January we added two software personnel and both have recently taken almost a month long vacation. Our policy is two weeks vacation after a year, accrued monthly. The head of software authorized these vacations because he says that you cannot make "software" types follow rules and he is afraid of losing them. The entire department comes in late and leaves early. The rest of the employees of course see this and it is causing dissension. How should management handle this?