Users configuring file system settings with a special subdirectory, such as this:
FileSystem Settings

should be aware that this will be considered the "root" in the IMCE configuration profile. Go into the IMCE configuration profile editor:
IMCE Config Profile

Use the (.) "period" or "dot" to set the root level directory to match the directory set in the file system settings, as shown:
IMCE Path Config

If you put in, for example, "public-files" instead of a (.) dot, then the system will create a NEW "public-files" folder under the existing "public-files" folder.

It can be quite confusing to debug.