I’m not sure if my problem was exactly the same as the other posters here but during my searches I kept coming across this thread which doesn’t really have a solution, so I’m posting this in the hope that it might help someone else out. I solved mine simply by recreating the asset directory structure within the subdirectory.
After literally hours of searching and despair I decided to actually read the notes for "File base path" in the manager, and it says:
NOTE: The File Browser directory must contain the subfolders images, files, flash and media in order for the file browser to function correctly.
So now my folder structure looks something like:
root
assets
images
mysubdirectory
images
myimage.jpg
files
flash
media
files
flash
media
etc...
manager
Now my manager users can upload and insert images and only ever see what’s in their own folder and now TinyMCE is happy, although I also had to make sure the maximum upload size was set large enough.
I’m no PHP guru, so if any MODx pros here can see a downside (esp security wise) to this method could you PLEASE TELL ME.