If you still have access to your media files, then you can ignore the warnings.
If not, then first check that ckgedit/fckeditor/userfiles[/m] is writable by the web server. If it is, then it's possible that for some reason you have directories or files by the same names in the [m]userfiles[/m] directory. If your wiki is on a unix machine or you are using the [m]nix_style[/m] option on a windows machine, remove the files/directories by the same names from [m]userfiles
and create new symbolic links to the media directory in userfiles.
llnk -s <path to your media directory> image
llnk -s <path to your media directory> file
If you can't do that, then go to data/meta/fck[/m]l and delete the file named [m]symchk.meta
and then reinstall ckgedit.
If your wiki is on a unix machine and the above solutions fail, or if you are on a windows machine, then go to the ckgedit configuration options in the configuration manager and select the winstyle