Last November I had LLETZ for CIN1 and went back 6 months later (May 2014) for 6 month smear. Like you the smear was clear but HPV still present.
I went back for a colposcopy last week (Sept 2014) and they decided not to repeat the smear but just to have a look and it seemed in my case that some mild changes were still visible. No biopsy was taken but they're just leaving it for 6 months to see if it clears up on its own.
I was told during the consultation before the examination that if everything looked OK they might just want to see me every year for smear tests.
I agree though, it is very confusing and I think some of the confusion is because HPV testing is a relatively new thing. I presume that in the past they would have just done a smear test at 6 months and if it was clear they'd have put you straight onto annual smears for a while and you wouldn't have known that the HPV was still there.
I think yes, your immune system would ideally fight off the HPV virus but it could just be that it is taking a bit longer to do that. I was advised to 'boost my immune system' by taking vitamin C and drinking green tea. Not sure how big a difference these things make but I already take strong vitamins so I'm happy to add in some extar vitamin C and some zinc.
When is your next colposcopy appointment?