I see this sort of thing ocasionally with FW tanks that are trying to cycle or have had their cycle disrupted. It sounds like you have enough of the nitrite-eating bacteria to keep up with the extra nitrite being produced by the extra ammonia, but not enough ammonia-eating bacteria to keep up with the ammonia itself. What ammonia is being changed to nitrite is being just as quickly changed to nitrate, thus the 0 nitrite reading but the overload of nitrate (from the overload of ammonia.)
I would suspect a dead organism somewhere. Maybe when you set up the refugium you had hitchhikers which subsequently died off.