Maybe. I learned a long time ago that degrees mean nothing. One of my best hires had no degree at all. Another had one in education. However, all things being equal, I would go for the candidate with a masters in CS over one in IT. I probably would prefer a musician. I know this is unreasonable, but I tend to regard business sounding degrees as the triumph of form over substance.

Also, is there a difference in quality or reputation between the two schools?