Roaming Profiles issue in 2003 server

My company had to move the profiles for all user accounts to another system. For the interm duration the roaming profiles have been returned to local. However the Application Data folder for some but not all users seems to return to the previous profile folder location. Ever once we've moved the destination folder for the new profiles the Application Data folder returns to the previous location. We also have the home directory going to the same location as the profiles. Any ideas what the issue can be?