I seem to be spending my time sorting out issues with Backup Clean up on WHS V1. One thing I have found that really helps is a tip originally published at http://social.microsoft.com/Forums/en-US/whsfaq/thread/b5372407-1f24-4eff-9092-069c4b4f0cee
In this post Ken Warren provides a very used command script you can run on your WHS to check all the drives individually (a tricky task with Drive Pooling)
You can use the following batch file to force chkdsk on all your drives. Copy the code below and paste it into notepad, then save it (on your server) as e.g. “checkall.cmd”:
net stop pdl net stop whsbackup chkdsk D: /x /r chkdsk C: /x /r for /d %%1 in (C:\fs\*) do start chkdsk /x /r %%1
You will need to run this as administrator and reboot after it has finished. I have found it sorts out quite a few issues. Thanks Ken.