How do you clean a mod when Boss says it needs cleaning, but it says it doesn't have any dirty ITM or UDR?
And I also have a problem cleaning the unofficial patch for Battlehorn castle. It says it has 5 dirty ITM, and whenever I apply filter to it, it becomes highlighted in red, and I can't clean it for some reason.
BOSS doesn't "know" anything - it only tells you what the devs have written in the code. If a mod has a "dirty" message but nothing else, it means that no one knows the CRC, ITM, or UDR information.
As for BHC - check http://cs.elderscrolls.com/constwiki/index.php/TES4Edit_Cleaning_Guide#BattlehornCastleEnhanced.esp_Special_Cleaning_Instructions.
Oh, oops. Hmm. I'd go over to http://www.gamesas.com/index.php?/topic/1200914-list-tes4edit-cleaning-list/page__hl__tes4edit (it's the TES4Edit cleaning thread) and ask there - someone who's more knowledgeable than I can answer you. There aren't any special issues noted, so I'm not sure why it doesn't work for you.