3 of us in our group appear to have encountered a similar problem. I have mounting holes in the corners of a PCB. The mounting holes have pads on both top and bottom layers. They are given a value of GND. They are surrounded by a zone, which is also GND. Editing the pads, under Pad Properties>Clearance overrides and settings>Connections to copper zones is set to Solid. In PCBNEW, all appears as it should, but when the Gerbers were generated, the zones were relieved back from the pads. I have done this many times in the past successfully, but not this time. What am I missing?
And it helps always if you attach the zipped project (maybe cut down the board and leave only the connected holes and the zones if you fear espionage).
In the SCHEMATIC you need to add symbols for mounting holes and connect them to Gnd. You may have to mess with the Ref Designators to get them to match the PCB or just update the PCB from Sch and they will appear.