Are you manually creating new shared folders outside of the folders that WHS offers as shared data folders? Using Windows Exploer? If so, don't do it. WHS won't know about them and won't manage them. If you want those folders to function as "normal" WHS shared folders, create them from the WHS Management Console.
Sure, if you want to create a folder where you can transfer the installer for your new antivirus program, then manually create a share. But WHS won't manage that space for you, manage file permissions, do folder duplication, do disk balancing, or do any other WHS data management to that folder. Unless you have very specific reasons for creating shared folders from Explorer, then I suggest you let WHS create and manage your data folders.