Wait until my friend Scott comes online, he re-compiled the v4 exporter with the v6 headers as well as fixing a few bugs.
http://sgmod.crashespad.com/files/ExportMD36.zip)
It fixes that annoying texture path problem so now it always exports paths in the / format (use to always do \) and also removes the ending of the texture filename, e.g. you'll end up with models/mymodel/mytexture instead of the original models\mymodel\mytexture.jpg
Has 1 or 2 other fixes in it too :)