Jack from JJP made a big stink about this on a podcast a bit ago, basically saying that modders shouldn't infringe on the IP of the people he's licensed from. I don't know why he has to be involved, it should be between IP holders and those who are infringing but I am guessing he is covering his butt.
That being said, what is the deal with putting logos and other copyrighted material in your mods? I see people selling stuff with artwork, logos and such that I know they didn't license. Is everyone just flying under the radar? I've dealt with enough IP and licensing stuff in the graphic design world that I try to stay away from all licensing issues but it's hard to compete with someone selling items for a game that uses a licensed logo which they aren't licensing.