FranticFish - 7:24 am on Sep 15, 2013 (gmt 0)
Check out the link profile of the site whose links Google doesn't like (and use one of the paid link databases for this, not just Google or one of the free ones as their data is very incomplete).
You might find that this genuine-looking link is from a site that is judged to be a bad neighbourhood.
If you are satisfied that the links are genuine and the site is genuine I'd try to let Google know that they've got it wrong. It's hard enough to get links without disavowing freely given ones!