Are you sure of the numbers on what the school paid. I know that educational prices vary from the prices that apply to regular customers. Often, for example, Apple will give deep discounts or even free stuff to schools. In fact, that is how they originally got into schools so much more than other types of computers (we're talking the 1980s here).
When you talk about cost, you need to consider total cost of use. For example, Linux is free, but the setup (in theory) requires someone with a little more skill to set up, thus the cost of time and expertise needs to be factored in. Even then, when it comes to servers and networking, linux is a cheaper option than windows.
While the basic Windows setup may be a little faster and require less expertise, you must pay for the OS and a simple install will most likely be very insecure.
Additionally, Windows servers and networks require significantly more maintainance, including restarts and monitoring of sinister programs, such as spyware and viruses. I have several clients on Windows systems that have gotten their networks hit by viruses and it has cost them thousands of dollars to clean up. Also, Microsoft programs are notorious for needing crucial updates. The updating process, while simple for a home user, should be done with by a skilled person in an institution or business. Any conflicts caused by these updates can result in hours of very costly time spent by a technician.
While more costly in hardware, Mac networks are fairly easy to set up. They come with stuff you'd find common on Linux (apache, php, etc.) and their roots in *nix make them more stable than Windows. Because they don't get harmed by the same viruses and similar programs that are common on windows machines, they have a much lower ongoing cost. I have read in several places that use of macs in a business or institutional setting can be far less expensive because of the reduced need for skilled technician. I don't have firsthand experience with this when it comes to a client, but I can say that the several Macs I have in my office offer a far lower occurance of problems than the Windows or mixed networks of my clients.
There are several other reasons your school may pick one or the other for any one lab. For example, Macs are very common in the print industry, making it more important for a journalism student to be familiar with them. Also consider that a student is far less likely to bring in his own software from home and install it on a mac than a pc, keeping the systems a little more clean and easier to manage.
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