The clearance between a zone and a track/via/pad must be set somewhere. The “manual” says it’s under the Setup menu in the top menu bar, but there’s no Setup menu, at least on my copy of PCBNEW. There is a Board Setup under the File menu that appears to be the same thing. While I cannot find anything about a global clearance value from a zone, my board is correct.
Another engineer, doing another board, has this setback set too high and needs to change it. I can’t find this value on his board either.
bdh