You did not indicate if you are using a corporate BB but if you are you may be restricted on using third party apps. They will sometimes download but not show in any folders. If you are not on a BES then check all folders to see if they are in one you did not check. Make sure all applications are showing and not hidden. Unless you accidently deleted the new folder it should be there.
Try adding a new folder with the same name and see if the files you added show up. Also if you can add a folder with the same name it may indicate the original was deleted.
KB18370-Downloaded application or theme cannot be found on the BlackBerry smartphone but shows as installed in the applications list