Don't think it's the step-up rings as I just put a test roll using the same lens, step-up rings and ND filter on an F90x (instead of the Nikon F3 in question) and it was absolutely fine.
The link I sent was more of a reference rather than the actual step-up ring setup I have. After some testing, other than when using on a 24mm lens, the step up rings are OK.
The problem, it seems, is the Nikon F3 body. I did various test shots and took out some factors and introduced others to see the results. I think my F3 is in need of a CLA...
I will be switching to an F90x in the meanwhile. Thanks everyone for the suggestions.