Both are technically okay grammatically. The difference might be based on who is saying it. An administrator of student academic records- that is, someone with a liberal arts degree, who does not work directly with computers -would tend to use "on," since it is more literary-sounding.
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there is a difference. Use Microsoft SQL server as example, if something is in SQL server, it is inside the SQL (database) client. And if something is on SQL server, it is normally on the Microsoft server that has SQL server but not in SQL client.
I usually hear "in the server" for more technical and formal use. "On the server" is usually used when you don't need to sound as formal. Therefore, if you are going for a more formal way of using this phrase, use "in" instead of "on." Great question, though.