"I'm familiar with Matlab." if someone said "I'm acquainted with Matlab." I would assume that they meant they'd seen it once on someone else's computer and they knew that Matlab could be used to make pretty graphs, but they had no idea how to use it and they were trying to avoid saying that they didn't know anything about it.

You generally say that you are familiar with something. In this situation I would say I know Matlab

I would say "I'm acquainted with someone" and "I'm familiar with something"

"Familiar with" is better. Saying "I'm acquainted with Matlab" (not "acquaintance with", by the way) sounds strange to me. In general, someone is acquainted with a person.

You could also use some more synonims of Familiar as: skilled , qualified, capable, experienced, competent, trained [source: http://www.freethesaurus.com/proficient]