Thankyou.
Worked like a charm. I had thought I had tried all of the options, but I must have missed that one. This will save me much time, many thanks.
For anyone else with the same issue, the option can be found here: "Pad Properties" / "Local Clearance and Settings" / "Copper Zones" / "Pad Connection", and set to "Solid" (mine was originally to "From parent footprint"). There is no visual feedback in the preview, but it does work. Accept the change, update the footprints in pcbnew (via the footprint properties, then "Change Footprint", which can be used to update all footprints of a certain type), and then redo the copper pour ("B").