Duplicate entries of single TV Show

Hi all, I have a little bit of a pickle that I can't quite work out. My TV Shows are on a Windows Home Server which as you may be aware creates duplicates of files you wish to backup. My protocol is once a TV Show season is finished I back it up to DVD and move it to a folder that is not duplicated on the server. By doing this I can save space as duplicates are not created when I don't need them.

So a common folder structure would be:

/TV Shows/NCIS/Season 8
/Backed Up TV Shows/NCIS/Season 1...7

Now, MC adds both folders as their own TV Shows so in MC I have two copies of most of my shows. This doesn't seem to be a big problem BUT some of the shows that have this structure show up in XBMC as two copies of the same show and both with all seasons available in them (so not NCIS 1-7 and then 8 but both entries have 1-8 ).

I don't understand why one show would work fine with this structure e.g. Always Sunny but one show e.g. NCIS would not. Can anyone offer any advice on how to fix this?

Cheers,
Rhys

OK, now I feel like an idiot...

The way that I have fixed this is to delete all of the NFOs etc that MC created for both folders of NCIS. Then delete NCIS x2 from XBMC library. Then rebuild TV Shows in MC. Rescrape both NCIS folders and = 2 entries in MC as per usual but only 1 entry in XBMC . If anything changes will post up.