"Just so you know" It's more a phrase that intends to make sure the listener actually knows something. The speaker has some doubt as to whether the listener is aware yet. "I'm telling you this because you might not know already". It's not trying to explain the new item of information, just making sure the listener is aware of it.
As the posting etiquette requires, do you have a context for us ?
Can "just so you know" be a rude phrase anyway? I've read that it is simliar to Just Sayin', but Just Sayin' doesn't seem to be a rude phrase, I mean, it depends on the way you say that of course, but yeah. I don't know a good example of "Just so you know" to come up with, if someone could help me out, it would be great