[rstoyguy]

When you build a ROM, all files start out in the \windows directory. It is the j.o.b. of the initflashfiles.dat to copy the files where they need to be. (All of your initflashfiles.txt data get appended to the .dat file by buildos.) As far as the registry entries not matching where the files are placed, I can't help you there. But you may look at the registry entries again and see if they match after the data in the initflashfiles.txt is processed.

But when you cook a rom, ALL files start out in \windows. It is a waste of space, that is why the ppckitchen folks try to have most everything run out of windows. When I make an oem I try put them where a .cab install would have put them. This is just the way it is. You could always build your rom and install your files with UserCustomization if you do not want all the duplicates.