The problem is that there is metadata associated with the files on the mac, things like icons are the simplest example. There is no way to natively store that data in the PC format used on the USB drive so it is being encoded in those ._ files. I do not know how to make them go away in general, except you can blow them away in the terminal I guess. In most cases it won't matter but some older carbon applications won't survive that.
Sorry for the non-answer there may be some better suggestions.