It's tedious...but, after each "file" action, you need to go into the Account Settings and turn off sync for the folder into which you filed the item. At present, when you file, the destination folder is automatically turned "on" for synchronization with the device, which then acts like it always has -- conglomerating everything into the Messages view. So you must manually turn that off each time.
I know this issue has been passed forward to BlackBerry to hopefully see if they can do something about it in future releases. But, for now, that's the way it works.
Occam's Razor nearly always applies when troubleshooting technology issues!
If anyone has been helpful to you, please show your appreciation by clicking the button inside of their post. Please click here and read, along with the threads to which it links, for helpful information to guide you as you proceed. I always recommend that you treat your BlackBerry like any other computing device, including using a regular backup schedule...click here for an article with instructions.