Are you being served/helped?
In a British shop, you might hear ‘Are you being served?’ as an inquiry as to whether or not a shop assistant is attending your interest in buying something. (It was once the title of a British TV comedy show about a department store.) The response might be ‘Yes, thank you, someone’s already helping me’, but it’s just as likely to be something like, ‘No, I’m fine thanks.’
‘Can I help you to . . .’ can be an offer to pass some dish or other at a dinner table.
There’s one thing to be careful of with serve. It can also describe what a male animal does to a female animal for the purpose of breeding.
In this specific situation, being on a US college campus, the fact that your usage of "I'm being served" was most likely found to be funny because of the modern urban usage of of the phrase "you got served".
Among the younger generations, specifically those currently at college and younger, to be "served" also carries the meaning of being beaten badly at something. If you were playing basketball with some friends, and you lost the informal game while only scoring one or no baskets, the others present in the game might tell you that you "got served". In this particular example, the fact that you were standing in line to take care of some paperwork issues might have been assumed to be a case of you having to solve a problem with classes or a money issue... in which case you had been given a problem to take care of. By saying "I'm being served", you might have been misconstrued to mean that you were saying you had gotten a raw deal from the college, and you were there to take care of it.
I think in American English, we would more commonly say, "Have you been helped?" or "Are you being helped?"
You might be asked, "Have you been served?" at a restaurant. And if someone had already taken your food order, you could rightly answer, "I'm being served."
In addition to Barrie's caution, served can also mean the "delivery of a writ, summons, or other legal papers to the person required to respond to them." That is, you can be served papers. Then you could also say, "I have been served." (Maybe that's what was so funny about what you said... I don't see the terrible faux pas. That, or customer service is really dead!)