Used the Macro recorder to automate switching up all the uv chanels when you're using the rtt seam fix method described here: http://www.gamasutra.com/features/20061019/kojesta_01.shtml Run the script after you select the faces that have the offending seam in them...after you run the script adjust your uvs, then set up…
When I read that article I was thinking someone could write a script(s) to help this out, and look it has come to pass. Thanks! I'll try it out when I get some time.