I have created a share on the Filer and two folders on the same share.If i copy something to one folder it gets copied to the other folder automatically .
Did you create a share and point it to the same location (vol or qtree)? If so, that's why when it shows up in 1 location, its in the other. if you want to replicate between the 2, you can do a robocopy or some other mechanism.
