Sounds possibly like a black balance problem. What kind of camera were you using?
It would be ususal for the blacks to go off color just by switching in an ND filter unless the filter switch is somehow tied into the camera electronics (possible). White balance is tied into the filter selection in many professional cameras. Change the filter and you recall a different white balance register. It’s not likely, but possible that switching in your ND filter will recall a different setup on your camera. Otherwise there may be some discrepencies in the RGB gamma/flare settings within the camera. Hard to tell.
You might be able to correct the bad blacks using the 3-way color corrector within FCP. Use the eye dropper and select a color that should be pure black and see if FCP can pull the color in to an acceptable look. Use the eye dropper on the left color wheel for this. You might also need to tweak the mids and whites as well, but this should get you pretty close.
Tom