Why am I unable to load duplicate folders in RTC?

If you are using the RTC Eclipse plug-in to do the loading, then use the "Browse the components to select the folders to be loaded" load option.  The next page of the wizard has check boxes indicating which folders you want to load.  By default, the immediate child directories of the component are selected.  Check the component root directory itself, which will then load the component root directory as the root of the loaded tree.  This should eliminate any folder name conflicts (as long as your components have unique names).   If you are using one of the other RTC clients to do the loading, the details of the load operation differ, but the concept is the same.