I have experienced this error before but don't know the exact cause and unique solution for this error, i tried different options and it got fixed somehow. Have you tried using the consistency tool WCF_CC. Mostly the problem get resolved by fixing the repository manually.
I know in some other thread Leon Limson has explained it little bit, but i cannot find any real solution for these kind of error, hope someone from SAP shed more light on it.
Rgds,
Shobhit