There's a thread somewhere where Shane discusses accounts that can be disputed that don't have to be removed. I can't remember the details, but I think this falls into one of the exceptions. I have a CC with a $0 balance that has a dispute comment, but it is closed, so not precisely the same question.
ETA: This is for FHA. Not sure if it applies to conventional or other loan programs. http://ficoforums.myfico.com/t5/Mortgage-Loans/FHA-amp-disputed-accounts-official-policy-change/m-p/...
Starting Score: ~500 (12/01/2008)