Welcome to the I Hate TinyMCE club.
I don't know the answer to your question, but FYI, the search box at the upper right of the System Settings grid does a nice job of finding partial matches if they're in the name, key, or description, so you seldom have to wade through all the settings.
I looked for new_file_permissions in the code and found this:
- [#MODX-760], [#MODX-1528] Removed new_file_permissions and new_folder_permissions system settings from setup
One thing to check is the path in the modx_workspaces table. I'm not sure if TinyMCE uses it, but it's worth a check.
You might also check the paths in your media sources and any TinyMCE System Settings. System Settings have a way of hanging around when you remove a package and not getting updated when you reinstall it.